diff --git a/doc/Makefile b/doc/Makefile
index 4072e01c4a7b80e6de137ca86c54a4bfbb0fd136..6e6f36a3781fff1c532d07bcc677a5cd43eae4c6 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -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
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 1a4d2eb7797dd5fd085a29c5cb770c4d664d9f83..ac6bfee64a4d6460e1a02df3626eb4b309629590 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,9 +1,9 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="17 Jan 2018 version">
+<META NAME="docnumber" CONTENT="22 Feb 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
+<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
-17 Jan 2018 version :c,h4
+22 Feb 2018 version :c,h4
Version info: :h4
@@ -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
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 7eddcf9fe16ff3fbc8573e64e88135179d79b876..7679f5fd92abb7162004864b9515f8b62775aaf2 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -979,6 +979,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"lj/cut/coul/long (gikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
@@ -1012,7 +1013,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"reax"_pair_reax.html,
"rebo (oi)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
-"snap"_pair_snap.html,
+"snap (k)"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (giko)"_pair_sw.html,
"table (gko)"_pair_table.html,
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index bfb6ef390171f67cc4df16f5d1a4486d427cb469..604df6c1aef12c08e896f6617f97114b78e1055c 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -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
diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index 24c32c478a58f5cca2c2e0f592329db8033f9846..e85c0d818f5e767c3a240d12971d278c4ffb01fe 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -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.
diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html
index 99270c7276dc9fbc26a1b2bb823dde544d0913cd..8d9625e1bd0e926742f0283c5229880681f89431 100644
--- a/doc/src/USER/atc/man_add_molecule.html
+++ b/doc/src/USER/atc/man_add_molecule.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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 <small|large> <TAG> <GROUP_NAME> <br/>
</p>
<ul>
@@ -35,21 +33,21 @@ syntax</a></h2>
<li><GROUP_NAME> = 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>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html
index 95192034d94d4ab342a0a0a061fcba52bc5e59bf..9beded1b164d22c57f5800d62d258bf0867e9999 100644
--- a/doc/src/USER/atc/man_add_species.html
+++ b/doc/src/USER/atc/man_add_species.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify_AtC add_species <TAG> <group|type> <ID> <br/>
</p>
<ul>
@@ -35,21 +33,21 @@ syntax</a></h2>
<li><ID> = name of group or type number <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </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 atoms of a specified type or within 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>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html
index 3073c0f9209f52a9cfe50db2f602ae0067c3ec98..6725170928a49b0887e1e09e3fc1634b94666773 100644
--- a/doc/src/USER/atc/man_atom_element_map.html
+++ b/doc/src/USER/atc/man_atom_element_map.html
@@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency> <br/>
</p>
<ul>
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Cannot change map type after initialization. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>lagrangian </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html
index 18b0dcae6ed1a24446d77f7941d28e4cbe9db733..28bc90fa01c053c99983a594100b086ddd6b08a5 100644
--- a/doc/src/USER/atc/man_atom_weight.html
+++ b/doc/src/USER/atc/man_atom_weight.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC atom_weight <method> <arguments></p>
<ul>
<li><method> = <br/>
@@ -36,22 +34,22 @@ syntax</a></h2>
read_in: list of values for atoms are read-in from specified file <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>lattice </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html
index 718f8a433f1c4fb9164e5d910fc12fe11eb52c6d..ef787f53acc2632e066aaf14766b5df0ac350706 100644
--- a/doc/src/USER/atc/man_atomic_charge.html
+++ b/doc/src/USER/atc/man_atomic_charge.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC <include | omit> atomic_charge</p>
<ul>
<li><include | omit> = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc compute include atomic_charge </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Determines whether AtC tracks the total charge as a finite element field </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Required for: electrostatics </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>if the atom charge is defined, default is on, otherwise default is off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html
index 3e877355f15509602a2275c82351349043e8033b..61596d3b31899ea0a65cdd4332753b61b3436eeb 100644
--- a/doc/src/USER/atc/man_boundary.html
+++ b/doc/src/USER/atc/man_boundary.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC boundary type <atom-type-id></p>
<ul>
<li><atom-type-id> = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</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="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html
index 87696b8b43fc457da47d4f501d4f96d48a11a000..40b82f3f6113ba5b21416776a4927fc2f05de3de 100644
--- a/doc/src/USER/atc/man_boundary_dynamics.html
+++ b/doc/src/USER/atc/man_boundary_dynamics.html
@@ -7,36 +7,34 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args] <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>prescribed on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html
index 2e96330d6cf8a18f8c359c9c2f36a4dc063d10cc..7eb950f78e54c7dfd17f4f7121332a592265f236 100644
--- a/doc/src/USER/atc/man_boundary_faceset.html
+++ b/doc/src/USER/atc/man_boundary_faceset.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC boundary_faceset <is | add> [args] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p>fix_modify AtC boundary_faceset is obndy </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>This is only valid when fe_md_boundary is set to faceset. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html
index 3e78f12963f3c44e01c9ab71bcbff511fc02a3e8..0663dba176e57066ea8b878f5bf3b7b2e1280889 100644
--- a/doc/src/USER/atc/man_boundary_integral.html
+++ b/doc/src/USER/atc/man_boundary_integral.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index f4c33f5076bda70c594aa432904728fdf7b16eae..a731b09116dd2a9e7fb677b5fcc12b433023bdfa 100644
--- a/doc/src/USER/atc/man_consistent_fe_initialization.html
+++ b/doc/src/USER/atc/man_consistent_fe_initialization.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC consistent_fe_initialization <on | off></p>
<ul>
<li><on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Default is off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html
index c321605e884f97b6c3e65c2381bab5c0bbe9ce2a..690f0fcc986e9670071c54d30c5cdc70a1756601 100644
--- a/doc/src/USER/atc/man_contour_integral.html
+++ b/doc/src/USER/atc/man_contour_integral.html
@@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]></p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset</li>
<li>axis (string) : x or y or z </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html
index af0236f30ef24106a57f0c6f54a4566aa9ffcbea..900952ba0b39735f31d74d8a44b6c6fd80067667 100644
--- a/doc/src/USER/atc/man_control.html
+++ b/doc/src/USER/atc/man_control.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control">fix_modify AtC control </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control <physics_type> <solution_parameter> </p>
<p><br/>
</p>
@@ -46,22 +44,22 @@ syntax</a></h2>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p>
</div>
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html
index 805c12567a6054f50c454fcfd8410aa7614f0d18..8f4f48659561834285e915632ec4dd8802cb1f1a 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control momentum none <br/>
</p>
<p>fix_modify AtC control momentum rescale <frequency><br/>
@@ -44,21 +42,21 @@ syntax</a></h2>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html
index 301297f306b90c4c7e433820eb4b74bfff6e24d0..eab186f71502d82b1667487b8b6e9c621e887e57 100644
--- a/doc/src/USER/atc/man_control_thermal.html
+++ b/doc/src/USER/atc/man_control_thermal.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control thermal <control_type> <optional_args></p>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br/>
@@ -46,25 +44,25 @@ syntax</a></h2>
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none<br/>
rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p>
diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
index 8a511019f9dd0643446fd25a4b746147cf337d69..a337a495e0e3eaf2cedb69441267654cdb68316a 100644
--- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
+++ b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control thermal correction_max_iterations <max_iterations></p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for use with thermal physics using the fractional step method. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>correction_max_iterations is 20 </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html
index 15725073d35a6a2d1a14c8f8f761e77356fef70e..d54a2010342e783243cc0ab90f8010515c23a892 100644
--- a/doc/src/USER/atc/man_decomposition.html
+++ b/doc/src/USER/atc/man_decomposition.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC decomposition <type></p>
<ul>
<li><type> = <br/>
@@ -32,20 +30,20 @@ syntax</a></h2>
distributed_memory: only owned nodal information on processor <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>replicated_memory is appropriate for simulations were the number of nodes << number of atoms </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>replicated_memory </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html
index b14c14d86d5dfbf4ef71a635335f0717af98fa4a..ab454c16d271fa0e9ed02e186601f9c2cdc0259e 100644
--- a/doc/src/USER/atc/man_electron_integration.html
+++ b/doc/src/USER/atc/man_electron_integration.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)> <br/>
</p>
<ul>
@@ -32,20 +30,20 @@ syntax</a></h2>
</li>
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
</p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>implicit<br/>
subcycle_steps = 1 </p>
</div>
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html
index 3723cf98bf36d1bca05d04c3735f6e9a3209a2fd..d01253c4b3e574981cc3d2e32159a4639bd7bcd3 100644
--- a/doc/src/USER/atc/man_equilibrium_start.html
+++ b/doc/src/USER/atc/man_equilibrium_start.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC equilibrium_start <on|off></p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc equilibrium_start on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only needed before filtering is begun</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html
index 8f6533ad646beca2b91ad6415f23b6d0c187933a..4f1f5962d9f3956bd1be3bf7a41c6a028769b07e 100644
--- a/doc/src/USER/atc/man_extrinsic_exchange.html
+++ b/doc/src/USER/atc/man_extrinsic_exchange.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC extrinsic exchange <on|off></p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Switches energy exchange between the MD system and electron system on and off</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only valid for use with two_temperature type of AtC fix.</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html
index 06bca2b337f7ca62483bb861ef9d49e7f53f756b..e517dd4855d86a90fe95517bf3bb07a0c99425f1 100644
--- a/doc/src/USER/atc/man_fe_md_boundary.html
+++ b/doc/src/USER/atc/man_fe_md_boundary.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see for how to specify the faceset name. </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Interpolate. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html
index 2abd84d6cef4b3040e13ba674c4e5e6e3d0f1cc0..b8ba584816bc2b2fce453df4f12f2a3589378feb 100644
--- a/doc/src/USER/atc/man_fem_mesh.html
+++ b/doc/src/USER/atc/man_fem_mesh.html
@@ -1,24 +1,45 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>ATC: fix_modify AtC fem create mesh</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.3.9.1 -->
-<h1><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h1><h2><a class="anchor" name="syntax">
-syntax</a></h2>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="contents">
+
+<h3><a class="anchor" id="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p><ul>
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
-<h2><a class="anchor" name="examples">
-examples</a></h2>
-<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
-description</a></h2>
-Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
-restrictions</a></h2>
-creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
-related</a></h2>
-<h2><a class="anchor" name="default">
-default</a></h2>
-none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<h4><a class="anchor" id="examples">
+examples</a></h4>
+<p><code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <br/>
+</p>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<p>Creates a uniform mesh in a rectangular region</p>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>creates only uniform rectangular grids in a rectangular region</p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
+none
+<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address>
</body>
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index 975f87e9499be3d210da661bff02dfb556141eae..7a871f5c8141c7c8122919f0c2ea8b5abdfa27ca 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -7,45 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC filter scale <scale> <br/>
</p>
<ul>
<li>scale (real) = characteristic time scale of the filter <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC filter scale 10.0 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>0. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html
index 8d9dbd3d12d0ede718c312b2136e880a7d4e2f47..2711d128e9f945be4e7c65ad8e18be43b2b78d08 100644
--- a/doc/src/USER/atc/man_filter_type.html
+++ b/doc/src/USER/atc/man_filter_type.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC filter type <exponential | step | no_filter> <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC filter type exponential </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Specifies the type of time filter used. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No default. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html
index e710c28ed268d58d037396681f25cd87593d978f..7cc6cfea5bad5089cfbddab53036c75ed2fedd0f 100644
--- a/doc/src/USER/atc/man_fix_atc.html
+++ b/doc/src/USER/atc/man_fix_atc.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_atc">fix atc command </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix <fixID> <group> atc <type> <parameter_file></p>
<ul>
<li>fixID = name of fix</li>
@@ -38,15 +36,15 @@ syntax</a></h2>
<li>parameter_file = name of the file with material parameters. <br/>
note: Neither hardy nor field requires a parameter file </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
<code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
<code> fix AtC internal atc hardy </code> <br/>
<code> fix AtC internal atc field </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
<p>The following coupling example is typical, but non-exhaustive:<br/>
</p>
@@ -134,16 +132,16 @@ description</a></h2>
</li>
</ul>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
<p>Currently,</p>
<ul>
<li>the coupling is restricted to thermal physics</li>
<li>the FE computations are done in serial on each processor.</li>
</ul>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>fix_modify commands for setup: <br/>
</p>
<ul>
@@ -243,8 +241,8 @@ related</a></h2>
<li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
</ul>
<p>Note: a set of example input files with the attendant material files are included with this package </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html
index d8369a878533909d87a5695b7b8bc17186c4d537..42815def6bca896ee183505fb869a327908b5853 100644
--- a/doc/src/USER/atc/man_fix_flux.html
+++ b/doc/src/USER/atc/man_fix_flux.html
@@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC fix_flux <field> <face_set> <value | function></p>
<ul>
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
<li><face_set> = name of set of element faces </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only normal fluxes (Neumann data) can be prescribed. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html
index cf5c93590a2f561755953ffc56108911d1e13e4c..03cf86eb9220720940f1fae44257a3df93addd12 100644
--- a/doc/src/USER/atc/man_fix_nodes.html
+++ b/doc/src/USER/atc/man_fix_nodes.html
@@ -7,46 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC fix <field> <nodeset> <constant | function></p>
<ul>
<li><field> = field name valid for type of physics</li>
<li><nodeset> = name of set of nodes to apply boundary condition</li>
<li><constant | function> = value or name of function followed by its parameters </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
<code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Creates a constraint on the values of the specified field at specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html
index c16550742b89e24e77917fbbe5322276201d3fb0..b45b7dfb0101a117ca58cc7faf78b1eec80a3a06 100644
--- a/doc/src/USER/atc/man_hardy_computes.html
+++ b/doc/src/USER/atc/man_hardy_computes.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number> <br/>
</p>
<ul>
@@ -35,8 +33,8 @@ syntax</a></h2>
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> compute virial all stress/atom </code> <br/>
<code> fix_modify AtC computes add virial volume </code> <br/>
<code> fix_modify AtC computes delete virial </code> <br/>
@@ -44,20 +42,20 @@ examples</a></h2>
<code> compute centrosymmetry all centro/atom </code> <br/>
<code> fix_modify AtC computes add centrosymmetry number </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
Per-atom compute must be specified before corresponding continuum field can be requested <br/>
</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>See manual page for compute </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No defaults exist for this command </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html
index 1f55fd5e3702cb8cbaa4f3f59e4ab7e2ebf3657f..17903aabd0d913d0d0bb78b9998c7c4105df4fba 100644
--- a/doc/src/USER/atc/man_hardy_fields.html
+++ b/doc/src/USER/atc/man_hardy_fields.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC fields <all | none> <br/>
fix_modify AtC fields <add | delete> <list_of_fields> <br/>
</p>
@@ -56,24 +54,24 @@ syntax</a></h2>
type_concentration: volume fraction of a specific atom type <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC fields add velocity temperature </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
<code> fix_modify AtC fields none </code> <br/>
followed by <br/>
<code> fix_modify AtC fields add velocity temperature </code> <br/>
will only output the velocity and temperature fields. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>By default, no fields are output </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html
index 708fecbca1dedd4470e5b6e6e15090b37aec4a48..00935f0ae25968b2c633a068899e03917241edaf 100644
--- a/doc/src/USER/atc/man_hardy_gradients.html
+++ b/doc/src/USER/atc/man_hardy_gradients.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC gradients <add | delete> <list_of_fields> <br/>
</p>
<ul>
@@ -33,21 +31,21 @@ syntax</a></h2>
<li>fields (keyword) = <br/>
gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
<code> fix_modify AtC gradients delete velocity </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No gradients are calculated by default </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html
index 3d81b367dd0e59c39be54580b80069c147d84cf6..f97037784c73349cab27f1df5e1145ede359b7ce 100644
--- a/doc/src/USER/atc/man_hardy_kernel.html
+++ b/doc/src/USER/atc/man_hardy_kernel.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC kernel <type> <parameters></p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@@ -40,22 +38,22 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
<code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
- ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+ ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No default </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html
index d140cf6840e290a81e312aab76129992cf5ca5ed..79c1006c973eb515a8416bbfc47399f86e03621e 100644
--- a/doc/src/USER/atc/man_hardy_on_the_fly.html
+++ b/doc/src/USER/atc/man_hardy_on_the_fly.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC on_the_fly <bond | kernel> <optional on | off> <br/>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
</p>
@@ -32,24 +30,24 @@ syntax</a></h2>
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC on_the_fly bond on </code> <br/>
<code> fix_modify AtC on_the_fly kernel </code> <br/>
<code> fix_modify AtC on_the_fly kernel off </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
</p>
</div>
diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html
index ab0315cb65b179cf01b60309711d2d9c2ba87942..e51cbc9873a03ed584d3d4fde162cdc738f2b0c9 100644
--- a/doc/src/USER/atc/man_hardy_rates.html
+++ b/doc/src/USER/atc/man_hardy_rates.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC rates <add | delete> <list_of_fields> <br/>
</p>
<ul>
@@ -33,22 +31,22 @@ syntax</a></h2>
<li>fields (keyword) = <br/>
rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
<code> fix_modify AtC rates delete stress </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No rates are calculated by default </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html
index c0a0be38523ed357b7806b006574cd5a3f08e5c0..41ae06eb8c42f7c2afba2ca1362c9ef8361ada52 100644
--- a/doc/src/USER/atc/man_initial.html
+++ b/doc/src/USER/atc/man_initial.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_initial">fix_modify AtC initial </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC initial <field> <nodeset> <constant | function></p>
<ul>
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
<li><nodeset> = name of set of nodes to apply initial condition</li>
<li><constant | function> = value or name of function followed by its parameters </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets the initial values for the specified field at the specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html
index b15bf71aadd4950ab67ed17cc72e6801bf6992f4..dfa19474e5be9e6c314ca23eafa58da8ee50439b 100644
--- a/doc/src/USER/atc/man_internal_atom_integrate.html
+++ b/doc/src/USER/atc/man_internal_atom_integrate.html
@@ -7,30 +7,28 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC internal_atom_integrate <on | off> <code> fix_modify AtC internal_atom_integrate on </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>on for coupling methods, off for post-processors off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html
index 31bee57860ef0a2354101c7e0940eb894563e6ab..849e8f0671369f9c22f05ccd6190cbddf15e2746 100644
--- a/doc/src/USER/atc/man_internal_element_set.html
+++ b/doc/src/USER/atc/man_internal_element_set.html
@@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC internal_element_set <element-set-name></p>
<ul>
<li><element-set-name> = name of element set defining internal region, or off </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see atom_element_map_type and boundary </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html
index 172187c2982093bd0109f01ef7d1922af38403f2..7f10e1707679d2c7027ee0166369aebc4a6654d8 100644
--- a/doc/src/USER/atc/man_internal_quadrature.html
+++ b/doc/src/USER/atc/man_internal_quadrature.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify atc internal_quadrature <on | off> [region] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc internal_quadrature off </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
-<h2><a class="anchor" id="optional">
-optional</a></h2>
+<h4><a class="anchor" id="optional">
+optional</a></h4>
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </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>on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html
index 08ec827decfea21768afad0970b0049d3e74c071..92db590198a43fc753c5e8becf64e465021f0f59 100644
--- a/doc/src/USER/atc/man_kernel_function.html
+++ b/doc/src/USER/atc/man_kernel_function.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC kernel <type> <parameters></p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@@ -40,21 +38,21 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
- ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+ ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>No default </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html
index 5dadb9d7304aaa0b764905fccdae458483b170e9..fd845d0a712f1c6d6d49108d7a8a3fcb174e098b 100644
--- a/doc/src/USER/atc/man_localized_lambda.html
+++ b/doc/src/USER/atc/man_localized_lambda.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control localized_lambda <on|off> </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc control localized_lambda on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </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>Default is off. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html
index bb3f8cfde8d74941f02a99440fd7af7dfc8ab212..ade780ddee0faf5bc11c18be9b79860db2ce4aa5 100644
--- a/doc/src/USER/atc/man_lumped_lambda_solve.html
+++ b/doc/src/USER/atc/man_lumped_lambda_solve.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control lumped_lambda_solve <on|off> </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to use or not use lumped matrix for lambda solve </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>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html
index 01ca9d192b14dc79810663c15c6fed23a4a52e91..31c18b4f1f961a1d77b321a1775ba4f818f40b59 100644
--- a/doc/src/USER/atc/man_mask_direction.html
+++ b/doc/src/USER/atc/man_mask_direction.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC control mask_direction <direction> <on|off> </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to mask out certain dimensions from the atomic regulator </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>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html
index 5f543fc20ce7fba887ae571814dc6c6ee812745b..140b745f09b72e0c208e6d9ce49e084c4f2ea556 100644
--- a/doc/src/USER/atc/man_mass_matrix.html
+++ b/doc/src/USER/atc/man_mass_matrix.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mass_matrix <fe | md_fe></p>
<ul>
<li><fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc mass_matrix fe </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Default is off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html
index 9867e90f770c393c3af3014ce1acf4b1e732b62b..c31ab4938d6c5ad6befe8ae71d6540dce2a7d9b8 100644
--- a/doc/src/USER/atc/man_material.html
+++ b/doc/src/USER/atc/man_material.html
@@ -7,39 +7,37 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_material">fix_modify AtC material </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC material gap_region 2</code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets the material model in elementset_name to be of type material_id. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>All elements default to the first material in the material file. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html
index cf5ad52f608afa40783a30aee6885a14a79a86ad..25a5c2cdae60c930794721d86bd10b933566dfa2 100644
--- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html
+++ b/doc/src/USER/atc/man_mesh_add_to_nodeset.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
<ul>
<li><id> = id of FE nodeset to be added to</li>
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to add nodes to an already existing FE nodeset. </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>Coordinates are assumed to be in lattice units. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html
index efaf7f4307218a770a4b6b506fbbbd6495aae863..a7ee112614fb93652bb14dbf4707907607a84460 100644
--- a/doc/src/USER/atc/man_mesh_create.html
+++ b/doc/src/USER/atc/man_mesh_create.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p> <br/>
</p>
<ul>
@@ -32,21 +30,21 @@ syntax</a></h2>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Creates only uniform rectangular grids in a rectangular region </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html
index 51bdae4faa022bd9a314818a9adce2bf90b9f943..2ac383a974bc37de6749eb0b12e1de53c81eda8f 100644
--- a/doc/src/USER/atc/man_mesh_create_elementset.html
+++ b/doc/src/USER/atc/man_mesh_create_elementset.html
@@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
<ul>
<li><id> = id to assign to the collection of FE element</li>
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html
index 163a6b442c361fb79dad08d19db528c7464bccaf..e62a827a783333c6aa596d1e28efdac434c16704 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_box.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_box.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]</p>
<ul>
<li><id> = id to assign to the collection of FE faces</li>
@@ -32,19 +30,19 @@ syntax</a></h2>
<li><in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to assign an id to a set of FE faces. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>The default options are units = lattice and the use of outer faces </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_create_faceset_plane.html b/doc/src/USER/atc/man_mesh_create_faceset_plane.html
index 3ca1108d1a7a4b8cf869bcac1668afeeffb55404..b1969cb79dd899194e1b797e25eb56343f319236 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_plane.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]</p>
<ul>
<li><id> = id to assign to the collection of FE faces</li>
@@ -32,19 +30,19 @@ syntax</a></h2>
<li><val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to assign an id to a set of FE faces. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>The default option is units = lattice. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html
index 9d5d1556544c84d76d7ca7c8a1791f54388c163e..39bfffd1198c6715bfa5b9e04e5ca1716519e6a5 100644
--- a/doc/src/USER/atc/man_mesh_create_nodeset.html
+++ b/doc/src/USER/atc/man_mesh_create_nodeset.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
<ul>
<li><id> = id to assign to the collection of FE nodes</li>
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </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>Coordinates are assumed to be in lattice units. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html
index cc269c8e651d7c1ade24c3b38df1e8bcebcb7907..60a2fe59a1095934762d4c34b845b560e00a3175 100644
--- a/doc/src/USER/atc/man_mesh_delete_elements.html
+++ b/doc/src/USER/atc/man_mesh_delete_elements.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh delete_elements <element_set></p>
<ul>
<li><element_set> = name of an element set </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC delete_elements gap </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Deletes a group of elements from the mesh. </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>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
index 45d03fc98685de7878d36817e0e15c5fe262c382..d05429ebabbf811cd7fe5929aa7fdd3c205fd9ec 100644
--- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
+++ b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min></p>
<ul>
<li><nodeset_id> = id of desired nodeset from which to create elementset</li>
<li><elementset_id> = id to assign to the collection of FE element</li>
<li><max/min> = flag to choose either the maximal or minimal elementset </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>None. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Unless specified, the maximal element set is created </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html
index be1b4c194f4d83fc6bd273a7a621e8ed782c55d2..f768a29c41de56432542fa5febb8cc96782601af 100644
--- a/doc/src/USER/atc/man_mesh_output.html
+++ b/doc/src/USER/atc/man_mesh_output.html
@@ -7,39 +7,37 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh output <file_prefix> </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh output meshData </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>none </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html
index d5291d99db1d2f9f6ce74e125558cd9b69998469..46487fdce7e7be93fed9d32ca8d09c66c1467298 100644
--- a/doc/src/USER/atc/man_mesh_quadrature.html
+++ b/doc/src/USER/atc/man_mesh_quadrature.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh quadrature <quad></p>
<ul>
<li>quad = one of <nodal|gauss1|gauss2|gauss3|face> --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh quadrature face </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>(Re-)assigns the quadrature style for the existing mesh. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html
index a497a2ed041b6134f88c3dba12897ff2c72b15ed..e0571ccf88eef86cb6dbc8e336591df345d44bf8 100644
--- a/doc/src/USER/atc/man_mesh_read.html
+++ b/doc/src/USER/atc/man_mesh_read.html
@@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p></p>
<ul>
<li>filename = name of file containing mesh to be read</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </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>periodicity flags are false by default </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html
index 21754a1e683185f57d74ba98c83e1604f00e7fb3..756cf4992258b507e87a0f199bae5df16407398a 100644
--- a/doc/src/USER/atc/man_mesh_write.html
+++ b/doc/src/USER/atc/man_mesh_write.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC mesh write <filename></p>
<ul>
<li>filename = name of file to write mesh </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Writes a mesh to a text file. </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>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html
index 3b987f70ef14033a184eb6a73f2d58dec0a0c8fb..60fbfcd888555ae5fb7c79ea748455c7e8e9704c 100644
--- a/doc/src/USER/atc/man_momentum_time_integration.html
+++ b/doc/src/USER/atc/man_momentum_time_integration.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC time_integration <descriptor> <br/>
</p>
<ul>
@@ -33,24 +31,24 @@ syntax</a></h2>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc time_integration verlet </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html
index 3129ff30c9172e5bc3bb76031a626190b66edbdc..aec1d5d55ae33a6713dde6ab621c4c132ad108d4 100644
--- a/doc/src/USER/atc/man_output.html
+++ b/doc/src/USER/atc/man_output.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output">fix_modify AtC output </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
<ul>
<li>filename_prefix (string) = prefix for data files</li>
@@ -37,23 +35,23 @@ syntax</a></h2>
tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC output heatFE 100 </code> <br/>
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
<code> fix_modify AtC output index step </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<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>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>no default format output indexed by time </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html
index be259388ba8ac14125ae89d41070c2b65cf22647..54079027c5053a2ebe3d9c2b387b966a1287fa56 100644
--- a/doc/src/USER/atc/man_output_elementset.html
+++ b/doc/src/USER/atc/man_output_elementset.html
@@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC output volume_integral <eset_name> <field> {`</p>
<ul>
<li>set_name (string) = name of elementset to be integrated over</li>
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC output eset1 mass_density </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<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>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html
index db76c8008ec00dc62b103c45aa40168d667c004f..2fc6e0268169fb3f0f00308ecff8160882f8bba6 100644
--- a/doc/src/USER/atc/man_output_nodeset.html
+++ b/doc/src/USER/atc/man_output_nodeset.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC output nodeset <nodeset_name> <operation></p>
<ul>
<li>nodeset_name (string) = name of nodeset to be operated on</li>
@@ -32,20 +30,20 @@ syntax</a></h2>
sum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<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>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html
index d46dcb12340bf3a055fbfdab7dcbec0cff752532..2cb2cb6113383c34effad09f654a8f41d532b1cd 100644
--- a/doc/src/USER/atc/man_pair_interactions.html
+++ b/doc/src/USER/atc/man_pair_interactions.html
@@ -7,40 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC pair_interactions <on|off> <br/>
fix_modify AtC bond_interactions <on|off> <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC bond_interactions on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>include bonds and/or pairs in the stress and heat flux computations </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>pair interactions: on, bond interactions: off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html
index d69d74db1a617c444bde634b5e6d67f83fa6bf20..b6fabbb27c1613cf8cda041d04560d9c4458b1b3 100644
--- a/doc/src/USER/atc/man_poisson_solver.html
+++ b/doc/src/USER/atc/man_poisson_solver.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p></p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = perioidicity flags for x, y, z </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>creates only uniform rectangular grids in a rectangular region </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html
index 96168fccc769fce0a7d6e15c21e024f61a2500aa..5fc21282f68860c6726887df2e9916c9b8bfcfff 100644
--- a/doc/src/USER/atc/man_read_restart.html
+++ b/doc/src/USER/atc/man_read_restart.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC read_restart [file_name] <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC read_restart ATC_state </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Reads the current state of the fields from a named text-based restart file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html
index 054291efda0e20d1b4b7fbd9f633c173a38f2390..e6ad418de6871e7b4dab85dc02eede170bbf048d 100644
--- a/doc/src/USER/atc/man_remove_molecule.html
+++ b/doc/src/USER/atc/man_remove_molecule.html
@@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify_AtC remove_molecule <TAG> <br/>
</p>
<ul>
<li><TAG> = tag for tracking a molecule type <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC remove_molecule water </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Removes tag designated for tracking a specified set of molecules. <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>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html
index d1d249eb76b0a7ab764f04ee472bb23d44a9afbb..acea7a56074df6c0ed151296fcd1d1048abc1426 100644
--- a/doc/src/USER/atc/man_remove_source.html
+++ b/doc/src/USER/atc/man_remove_source.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC remove_source <field> <element_set></p>
<ul>
<li><field> = field name valid for type of physics</li>
<li><element_set> = name of set of elements </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Remove a domain source. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html
index ba94a52658f0213a4d586578e3e6e94336f7c180..561364518fe2033590626709f6fd1ac72b512c77 100644
--- a/doc/src/USER/atc/man_remove_species.html
+++ b/doc/src/USER/atc/man_remove_species.html
@@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify_AtC delete_species <TAG> <br/>
</p>
<ul>
<li><TAG> = tag for tracking a species <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC remove_species gold </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Removes tag designated for tracking a specified species. <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>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
index cb82f61bbb895659bb160ba0275583c34dfc0555..88e6748001c44716880a1b8a71b072d343e33d60 100644
--- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html
+++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
@@ -7,39 +7,37 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC reset_atomic_reference_positions </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc reset_atomic_reference_positions </code></p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p><code> </code></p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><code> </code></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p><code> Default is off </code></p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html
index 35d75ccb97798d0405d21d66a27ac7b9cb7bac68..a6429bf6d6c8b040f9171787f779ef49a9333768 100644
--- a/doc/src/USER/atc/man_reset_time.html
+++ b/doc/src/USER/atc/man_reset_time.html
@@ -7,55 +7,53 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC reset_time </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc reset_time 0.0 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Resets the simulation time counter. </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>
-<h2><a class="anchor" id="syntax">
-syntax</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>
+<h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC kernel_bandwidth </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc reset_time 8 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Only is used if kernel functions are being used. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Number of sample locations. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html
index 13f468b22289a4763292768c909843b58d1f865d..4e48c4bb299c854bb86f26adcb83d1a771725a3e 100644
--- a/doc/src/USER/atc/man_sample_frequency.html
+++ b/doc/src/USER/atc/man_sample_frequency.html
@@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC sample_frequency [freq]</p>
<ul>
<li>freq (int) : frequency to sample field in number of steps </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC sample_frequency 10 </code></p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><code> </code></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p><code> none </code></p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html
index d104e535b6bb1501d70aed3068403292a9fddb59..cf775c9b36d4e9a43abab0d2716c0a6d7c70a29d 100644
--- a/doc/src/USER/atc/man_set.html
+++ b/doc/src/USER/atc/man_set.html
@@ -7,46 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_set">fix_modify AtC set </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC set reference_potential_energy <value_or_filename(optional)></p>
<ul>
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
</li>
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC set reference_potential_energy </code> <br/>
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<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>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>Defaults to lammps zero point i.e. isolated atoms </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html
index 833b2a866f4d28ad552ea2c257022dd0a77baacc..c7239f2c412db0ac97ec56462ce96c93d1726c7e 100644
--- a/doc/src/USER/atc/man_source.html
+++ b/doc/src/USER/atc/man_source.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_source">fix_modify AtC source </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC source <field> <element_set> <value | function></p>
<ul>
<li><field> = field name valid for type of physics</li>
<li><element_set> = name of set of elements </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html
index 70f62d2e5739f6aaedbd6599052b23dfd8af31cf..3f43340af827c5c61162078843dd7b6af7116ff9 100644
--- a/doc/src/USER/atc/man_source_integration.html
+++ b/doc/src/USER/atc/man_source_integration.html
@@ -7,36 +7,34 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_source_integration">fix_modify AtC source_integration </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC source_integration < fe | atom> </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc source_integration atom </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<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="description">
+description</a></h4>
+<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>Default is fe </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html
index f4fb21471c634eae1f1c8cb30e1734fba745e877..a07ba29cab6f1780d61dfbc22bd0f5f50f3973b8 100644
--- a/doc/src/USER/atc/man_temperature_definition.html
+++ b/doc/src/USER/atc/man_temperature_definition.html
@@ -7,37 +7,35 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_temperature_definition">fix_modify AtC temperature_definition </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC temperature_definition <kinetic|total></p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc temperature_definition kinetic </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>kinetic </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html
index c2f636134f09d21311c85498570ff4b6078c56ac..fe293138be2a7206963a5c2339be637da3542e6e 100644
--- a/doc/src/USER/atc/man_thermal_time_integration.html
+++ b/doc/src/USER/atc/man_thermal_time_integration.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC time_integration <descriptor> <br/>
</p>
<ul>
@@ -33,23 +31,23 @@ syntax</a></h2>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc time_integration gear </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html
index ec70fed871761cfb327546273ea249c471bc98ba..732eaa3a36114c766118a0ab5aadd541e6284ab5 100644
--- a/doc/src/USER/atc/man_time_filter.html
+++ b/doc/src/USER/atc/man_time_filter.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_time_filter">fix_modify AtC filter </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC filter <on | off | equilibrate> <br/>
</p>
<ul>
@@ -32,22 +30,22 @@ syntax</a></h2>
</li>
<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc transfer filter on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a> <br/>
<a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html
index 8f729cffe3a802ec4334259e008d46692f13b65c..f5410816d75a779a6c6ec38c2e8bad1f64ac262f 100644
--- a/doc/src/USER/atc/man_track_displacement.html
+++ b/doc/src/USER/atc/man_track_displacement.html
@@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_track_displacement">fix_modify AtC track_displacement </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC track_displacement <on/off> <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc track_displacement on </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>Some constitutive models require the displacement field </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html
index b2a19a7fd0282edf2576a43777a89339c9d11a4b..95e1f4be5a85ea44cb7db7b434a0eb053262b9b4 100644
--- a/doc/src/USER/atc/man_unfix_flux.html
+++ b/doc/src/USER/atc/man_unfix_flux.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_unfix_flux">fix_modify AtC unfix_flux </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC fix_flux <field> <face_set> <value | function></p>
<ul>
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
<li><face_set> = name of set of element faces </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html
index 498d549f9eb6dc1a34532f1a35e502ae483181c5..78495c928a4751e188868ade7b93cbfb6496b04b 100644
--- a/doc/src/USER/atc/man_unfix_nodes.html
+++ b/doc/src/USER/atc/man_unfix_nodes.html
@@ -7,43 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_unfix_nodes">fix_modify AtC unfix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC unfix <field> <nodeset></p>
<ul>
<li><field> = field name valid for type of physics</li>
<li><nodeset> = name of set of nodes </li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC unfix temperature groupNAME </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Removes constraint on field values for specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html
index 939506a28e8dd71c68192c5a45758824dedb9d99..8a0e5b62a81bb9488e6bf5e9e6f61dbfc929fef3 100644
--- a/doc/src/USER/atc/man_write_atom_weights.html
+++ b/doc/src/USER/atc/man_write_atom_weights.html
@@ -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>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_write_atom_weights">fix_modify AtC write_atom_weights </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC write_atom_weights <filename> <frequency></p>
<ul>
<li><filename> = name of file that atomic weights are written to <br/>
@@ -32,19 +30,19 @@ syntax</a></h2>
<li><frequency> = how often writes will occur <br/>
</li>
</ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Command for writing the values of atomic weights to a specified file. </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>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
<a href="http://www.doxygen.org/index.html">
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html
index 6ea350d5e859a3985dce72e47445c9cc583024f0..6dca57673bbdabe393ad0fa2512f8c566a1f4374 100644
--- a/doc/src/USER/atc/man_write_restart.html
+++ b/doc/src/USER/atc/man_write_restart.html
@@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<center>
+ <a href="http://lammps.sandia.gov">LAMMPS Website</a>
+ <a href="../../Manual.html">LAMMPS Manual</a>
+ <a href="../../fix_atc.html">USER-AtC Manual</a>
+ <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 Page</span></a></li>
- <li class="current"><a href="pages.html"><span>Related 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_write_restart">fix_modify AtC write_restart </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
<p>fix_modify AtC write_restart [file_name] <br/>
</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
<p><code> fix_modify AtC write_restart restart.mydata </code> <br/>
</p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
<p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
diff --git a/doc/src/body.txt b/doc/src/body.txt
index 54ec157c744b4a18b89e318651b25d385c53c45e..344e5b1d6597c4440125a7225d345ae412c33a27 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -6,7 +6,7 @@
:line
-Body particles :h3
+Body particles :h1
[Overview:]
diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt
index 75a82f063ade59000a7cfa02cf89225a3a099d4c..49014f0591ff08e6f6e636067eed11ee9c8aab43 100644
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@@ -90,13 +90,11 @@ likewise for this post-processing example:
run 1000 :pre
the mesh's linear interpolation functions can be used as the localization function
- by using the field option:
+by using the field option:
fix AtC internal atc field
-
fix_modify AtC mesh create 1 1 1 box p p p
-
- ...
+ ... :pre
Note coupling and post-processing can be combined in the same simulations using separate fixes.
@@ -108,11 +106,10 @@ No information about this fix is written to "binary restart files"_restart.html.
[Restrictions:]
-Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
+Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently:
-Currently,
-- the coupling is restricted to thermal physics
-- the FE computations are done in serial on each processor. :ul
+the coupling is restricted to thermal physics :ulb,l
+the FE computations are done in serial on each processor. :l,ule
[Related commands:]
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index c78142a99991a47fa5033f1f384f591effc312c0..38f0fb95ce0530d425689b0daa9052e6a6995074 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -95,8 +95,8 @@ which will result in roughly one MC move per atom or molecule
per MC cycle.
All inserted particles are always added to two groups: the default
-group "all" and the fix group specified in the fix command (which can
-also be "all"). In addition, particles are also added to any groups
+group "all" and the fix group specified in the fix command.
+In addition, particles are also added to any groups
specified by the {group} and {grouptype} keywords. If inserted
particles are individual atoms, they are assigned the atom type given
by the type argument. If they are molecules, the type argument has no
@@ -104,6 +104,12 @@ effect and must be set to zero. Instead, the type of each atom in the
inserted molecule is specified in the file read by the
"molecule"_molecule.html command.
+NOTE: Care should be taken to apply fix gcmc only to
+a group that contains only those atoms and molecules
+that you wish to manipulate using Monte Carlo.
+Hence it is generally not a good idea to specify
+the default group "all" in the fix command, although it is allowed.
+
This fix cannot be used to perform GCMC insertions of gas atoms or
molecules other than the exchanged type, but GCMC deletions,
and MC translations, and rotations can be performed on any atom/molecule in
diff --git a/doc/src/group.txt b/doc/src/group.txt
index afa218c5a34880aa0ef71935be0d1f825fd79c08..dddb0459e3711e526e6077318aa6ae51922b0196 100644
--- a/doc/src/group.txt
+++ b/doc/src/group.txt
@@ -13,11 +13,13 @@ group command :h3
group ID style args :pre
ID = user-defined name of the group :ulb,l
-style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
+style = {delete} or {clear} or {empty} or {region} or \
+ {type} or {id} or {molecule} or {variable} or \
{include} or {subtract} or {union} or {intersect} or \
{dynamic} or {static} :l
{delete} = no args
{clear} = no args
+ {empty} = no args
{region} args = region-ID
{type} or {id} or {molecule}
args = list of one or more atom types, atom IDs, or molecule IDs
@@ -41,6 +43,7 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
keyword = {region} or {var} or {every}
{region} value = region-ID
{var} value = name of variable
+ {property} value = name of per-atom property
{every} value = N = update group every this many timesteps
{static} = no args :pre
:ule
@@ -99,6 +102,10 @@ e.g. using the "run every"_run.html command if a fix or compute or
other operation expects the atoms in the group to remain constant, but
LAMMPS does not check for this.
+The {empty} style creates an empty group, which is useful for commands
+like "fix gcmc"_fix_gcmc.html or with complex scripts that add atoms
+to a group.
+
The {region} style puts all atoms in the region volume into the group.
Note that this is a static one-time assignment. The atoms remain
assigned (or not assigned) to the group even in they later move out of
@@ -215,7 +222,11 @@ conditions are applied. If the {region} keyword is used, atoms not in
the specified region are removed from the dynamic group. If the {var}
keyword is used, the variable name must be an atom-style or
atomfile-style variable. The variable is evaluated and atoms whose
-per-atom values are 0.0, are removed from the dynamic group.
+per-atom values are 0.0, are removed from the dynamic group. If the {property}
+keyword is used, the per-atom property name must be a previously defined
+per-atom property. The per-atom property is evaluated and atoms whose
+values are 0.0 are removed from the dynamic group, otherwise they
+are added to the group.
The assignment of atoms to a dynamic group is done at the beginning of
each run and on every timestep that is a multiple of {N}, which is the
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 492f42e4d9336000d0e51bcd4c4dff81414ebd1e..63741cb57f10f0f1f29db19e81084a687fbdde98 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -20,6 +20,7 @@ Section_python.html
Section_errors.html
Section_history.html
+lammps_tutorials.html
tutorial_bash_on_windows.html
tutorial_drude.html
tutorial_github.html
@@ -28,6 +29,7 @@ tutorial_pylammps.html
body.html
manifolds.html
+lammps_commands.html
angle_coeff.html
angle_style.html
atom_modify.html
@@ -138,7 +140,6 @@ fix_adapt_fep.html
fix_addforce.html
fix_addtorque.html
fix_append_atoms.html
-fix_atc.html
fix_atom_swap.html
fix_ave_atom.html
fix_ave_chunk.html
@@ -277,6 +278,7 @@ fix_spring_self.html
fix_srd.html
fix_store_force.html
fix_store_state.html
+fix_surface_global.html
fix_temp_berendsen.html
fix_temp_csvr.html
fix_temp_rescale.html
@@ -423,11 +425,13 @@ pair_airebo.html
pair_awpmd.html
pair_beck.html
pair_body.html
+pair_body_rounded_polygon.html
pair_bop.html
pair_born.html
pair_brownian.html
pair_buck.html
pair_buck_long.html
+pair_buck6d_coul_gauss.html
pair_charmm.html
pair_class2.html
pair_colloid.html
@@ -539,6 +543,7 @@ bond_zero.html
angle_charmm.html
angle_class2.html
angle_cosine.html
+angle_cosine_buck6d.html
angle_cosine_delta.html
angle_cosine_periodic.html
angle_cosine_shift.html
@@ -578,11 +583,13 @@ improper_distance.html
improper_fourier.html
improper_harmonic.html
improper_hybrid.html
+improper_inversion_harmonic.html
improper_none.html
improper_ring.html
improper_umbrella.html
improper_zero.html
+fix_atc.html
USER/atc/man_add_molecule.html
USER/atc/man_add_species.html
USER/atc/man_atom_element_map.html
diff --git a/doc/src/lammps_commands.txt b/doc/src/lammps_commands.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9c2e7366a1d1c116096b337e6b1a7f98281a4ef
--- /dev/null
+++ b/doc/src/lammps_commands.txt
@@ -0,0 +1,10 @@
+
+LAMMPS Commands :h1
+
+The following pages contain the detailed documentation of all
+LAMMPS commands included in this version of LAMMPS. Generic
+commands are listed first (in alphabetical order) followed by
+command categories like compute styles or pair styles and so on.
+
+The documentation for the USER-ATC package fix_modify commands
+follow at the very end of this manual.
diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ceda65b600744e9133168348bcc55ea78629bfc
--- /dev/null
+++ b/doc/src/lammps_tutorials.txt
@@ -0,0 +1,6 @@
+
+Tutorials :h2
+
+The following pages contain some in-depth tutorials for
+selected topics, that did not fit into any other place
+in the manual.
diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt
index c9bb1ce57f850242b8940365a4a4cebfff4fa162..36c6caacb7d81262910f53f80bf8c384696f5a88 100644
--- a/doc/src/manifolds.txt
+++ b/doc/src/manifolds.txt
@@ -6,7 +6,7 @@
:line
-Manifolds (surfaces) :h3
+Manifolds (surfaces) :h1
[Overview:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index 058d54fb5950aec706e4de4b4561cb23f924b5e9..e297d479bc3ae16d3054130ba67d9bb7fe3a0a97 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -32,6 +32,8 @@ pair_style lj/cut/coul/long/omp command :h3
pair_style lj/cut/coul/msm command :h3
pair_style lj/cut/coul/msm/gpu command :h3
pair_style lj/cut/coul/msm/omp command :h3
+pair_style lj/cut/coul/wolf command :h3
+pair_style lj/cut/coul/wolf/omp command :h3
pair_style lj/cut/tip4p/cut command :h3
pair_style lj/cut/tip4p/cut/omp command :h3
pair_style lj/cut/tip4p/long command :h3
@@ -63,6 +65,10 @@ args = list of arguments for a particular style :ul
{lj/cut/coul/msm} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ {lj/cut/coul/wolf} args = alpha cutoff (cutoff2)
+ alpha = damping parameter (inverse distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@@ -115,6 +121,10 @@ pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
+pair_style lj/cut/coul/wolf 0.2 5. 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 2.5 :pre
+
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
@@ -179,6 +189,24 @@ that a term is added for the "core/shell
model"_Section_howto.html#howto_25 to allow charges on core and shell
particles to be separated by r = 0.0.
+Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf
+summation method, described in "Wolf"_#Wolf1, given by:
+
+:c,image(Eqs/pair_coul_wolf.jpg)
+
+where {alpha} is the damping parameter, and erfc() is the
+complementary error-function terms. This potential
+is essentially a short-range, spherically-truncated,
+charge-neutralized, shifted, pairwise {1/r} summation. With a
+manipulation of adding and subtracting a self term (for i = j) to the
+first and second term on the right-hand-side, respectively, and a
+small enough {alpha} damping parameter, the second term shrinks and
+the potential becomes a rapidly-converging real-space summation. With
+a long enough cutoff and small enough alpha parameter, the energy and
+forces calculated by the Wolf summation method approach those of the
+Ewald sum. So it is a means of getting effective long-range
+interactions with a short-range potential.
+
Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P
water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless
site located a short distance away from the oxygen atom along the
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index 8c9aa02e22c37f52e4f048476eb8948ef0043c3f..4ea60163b2214c35c0328975f33c97664c19635d 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -547,7 +547,7 @@ charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
dpd: atom-ID atom-type theta x y z
edpd: atom-ID atom-type edpd_temp edpd_cv x y z
-mdpd: atom-ID atom-type x y z
+mdpd: atom-ID atom-type rho x y z
tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt
index 52eb6415db8415c04b2c07395e9e7ef3c508af6c..11cddb3cbf3fa7abc4350c9fe0cfb685f19b7b47 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@@ -6,14 +6,14 @@
:line
-PyLammps Tutorial :h1
+PyLammps Tutorial :h3
<!-- RST
.. contents::
END_RST -->
-Overview :h2
+Overview :h4
PyLammps is a Python wrapper class which can be created on its own or use an
existing lammps Python object. It creates a simpler, Python-like interface to
@@ -23,16 +23,16 @@ C++ code implementation. Finally, the IPyLammps wrapper builds on top of
PyLammps and adds some additional features for IPython integration into IPython
notebooks, e.g. for embedded visualization output from dump/image.
-Comparison of lammps and PyLammps interfaces :h3
+Comparison of lammps and PyLammps interfaces :h5
-lammps.lammps :h4
+lammps.lammps :h6
uses C-Types
direct memory access to native C++ data
provides functions to send and receive data to LAMMPS
requires knowledge of how LAMMPS internally works (C pointers, etc) :ul
-lammps.PyLammps :h4
+lammps.PyLammps :h6
higher-level abstraction built on top of original C-Types interface
manipulation of Python objects
@@ -41,11 +41,11 @@ shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
-Quick Start :h2
+Quick Start :h4
-System-wide Installation :h3
+System-wide Installation :h5
-Step 1: Building LAMMPS as a shared library :h4
+Step 1: Building LAMMPS as a shared library :h6
To use LAMMPS inside of Python it has to be compiled as shared library. This
library is then loaded by the Python interface. In this example we enable the
@@ -60,7 +60,7 @@ make yes-MOLECULE :pre
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre
-Step 2: Installing the LAMMPS Python package :h4
+Step 2: Installing the LAMMPS Python package :h6
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation.
@@ -71,12 +71,12 @@ python install.py :pre
NOTE: Recompiling the shared library requires reinstalling the Python package
-Installation inside of a virtualenv :h3
+Installation inside of a virtualenv :h5
You can use virtualenv to create a custom Python environment specifically tuned
for your workflow.
-Benefits of using a virtualenv :h4
+Benefits of using a virtualenv :h6
isolation of your system Python installation from your development installation
installation can happen in your user directory without root access (useful for HPC clusters)
@@ -87,7 +87,7 @@ you can even install specific old versions of a package if necessary :ul
apt-get install python-virtualenv :pre
-Creating a virtualenv with lammps installed :h4
+Creating a virtualenv with lammps installed :h6
# create virtualenv name 'testing' :pre
@@ -107,7 +107,7 @@ source testing/bin/activate :pre
(testing) deactivate :pre
-Creating a new instance of PyLammps :h2
+Creating a new instance of PyLammps :h4
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new {lammps} instance is created.
@@ -121,7 +121,7 @@ from lammps import lammps, PyLammps
lmp = lammps()
L = PyLammps(ptr=lmp) :pre
-Commands :h2
+Commands :h4
Sending a LAMMPS command with the existing library interfaces is done using
the command method of the lammps object instance.
@@ -155,7 +155,7 @@ them automatically to a final command string.
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre
-System state :h2
+System state :h4
In addition to dispatching commands directly through the PyLammps object, it
also provides several properties which allow you to query the system state.
@@ -208,7 +208,7 @@ List of groups present in the current system :dd
:dle
-Working with LAMMPS variables :h2
+Working with LAMMPS variables :h4
LAMMPS variables can be both defined and accessed via the PyLammps interface.
@@ -229,7 +229,7 @@ property of this object.
print(a.value)
a.value = 4 :pre
-Retrieving the value of an arbitrary LAMMPS expressions :h2
+Retrieving the value of an arbitrary LAMMPS expressions :h4
LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
@@ -240,7 +240,7 @@ result = L.eval("pe") # potential energy :pre
result = L.eval("v_t/2.0") :pre
-Accessing atom data :h2
+Accessing atom data :h4
All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
@@ -263,7 +263,7 @@ L.atoms\[0\].position = (1.0, 0.0) :pre
# set position in 3D simulation
L.atoms\[0\].position = (1.0, 0.0, 1.) :pre
-Evaluating thermo data :h2
+Evaluating thermo data :h4
Each simulation run usually produces thermo output based on system state,
computes, fixes or variables. The trajectories of these values can be queried
@@ -291,7 +291,7 @@ steps = L.runs\[0\].step
ke = L.runs\[0\].ke
plt.plot(steps, ke) :pre
-Error handling with PyLammps :h2
+Error handling with PyLammps :h4
Compiling the shared library with C++ exception support provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
@@ -304,7 +304,7 @@ current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
-Using PyLammps in IPython notebooks and Jupyter :h2
+Using PyLammps in IPython notebooks and Jupyter :h4
If the LAMMPS Python package is installed for the same Python interpreter as
IPython, you can use PyLammps directly inside of an IPython notebook inside of
@@ -320,7 +320,7 @@ Python environment (this assumes you followed the Quick Start instructions):
jupyter notebook :pre
-IPyLammps Examples :h2
+IPyLammps Examples :h4
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
@@ -328,7 +328,7 @@ directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
-Validating a dihedral potential :h3
+Validating a dihedral potential :h5
This example showcases how an IPython Notebook can be used to compare a simple
LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
@@ -353,7 +353,7 @@ plot inside the IPython notebook.
:c,image(JPG/pylammps_dihedral.jpg)
-Running a Monte Carlo relaxation :h3
+Running a Monte Carlo relaxation :h5
This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
simulation, computing and plotting energy terms and even embedding video output.
@@ -424,7 +424,7 @@ The energies of each iteration are collected in a Python list and finally plotte
The IPython notebook also shows how to use dump commands and embed video files
inside of the IPython notebook.
-Using PyLammps and mpi4py (Experimental) :h2
+Using PyLammps and mpi4py (Experimental) :h4
PyLammps can be run in parallel using mpi4py. This python package can be installed using
@@ -451,7 +451,7 @@ mpirun -np 4 python melt.py :pre
IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
-Feedback and Contributing :h2
+Feedback and Contributing :h4
If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index e3b7c5de0d6a50ac158d167365e976cacb396e58..c0851464c3f14e11629b8e65ee58a171499a4e45 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -689,7 +689,7 @@ increase in increments of z, starting at x, until a is reached. At
that point the timestep increases in increments of c, from a to b,
then after b, increments by z are resumed until y is reached. For any
current timestep, the next timestep in the sequence is returned. Thus
-if stride(1000,2000,100,1350,1360,1) is used in a variable by the
+if stride2(1000,2000,100,1350,1360,1) is used in a variable by the
"dump_modify every"_dump_modify.html command, it will generate the
sequence of output timesteps:
diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/meso/edpd/in.edpd
index 316099bce35ceb0f7e7fd370cf0862fd8c433804..af1a79d73daec55199bb3a5b835762a279e0b286 100644
--- a/examples/USER/meso/edpd/in.edpd
+++ b/examples/USER/meso/edpd/in.edpd
@@ -1,54 +1,54 @@
-########################################################################
-### Heat conduction analog of periodic Poiseuille flow problem ###
-### using energy-conserving DPD (eDPD) simulation ###
-### ###
-### Created : Zhen Li (zhen_li@brown.edu) ###
-### Division of Applied Mathematics, Brown University. ###
-### ###
-### mDPD system setup follows Fig.12 in the publication: ###
-### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
-### "Energy-conserving dissipative particle dynamics with ###
-### temperature-dependent properties". J. Comput. Phys., ###
-### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
-########################################################################
-units lj
-dimension 3
-boundary p p p
-neighbor 0.2 bin
-neigh_modify every 1 delay 0 check yes
-
-atom_style edpd
-
-region edpd block -10 10 -10 10 -5 5 units box
-create_box 1 edpd
-create_atoms 1 random 16000 276438 NULL
-mass 1 1.0
-set atom * edpd/temp 1.0
-set atom * edpd/cv 1.0E5
-
-pair_style edpd 1.58 9872598
-#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
-pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
- power 10.54 -3.66 3.44 -4.10 &
- kappa -0.44 -3.21 5.04 0.00
-
-compute mythermo all temp
-thermo 100
-thermo_modify temp mythermo
-thermo_modify flush yes
-
-velocity all create 1.0 432982 loop local dist gaussian
-
-fix mvv all mvv/edpd 0.5
-fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
-fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
-
-timestep 0.01
-run 500
-reset_timestep 0
-
-compute temp all edpd/temp/atom
-compute ccT all chunk/atom bin/1d y 0.0 1.0
-fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
-
-run 500
+########################################################################
+### Heat conduction analog of periodic Poiseuille flow problem ###
+### using energy-conserving DPD (eDPD) simulation ###
+### ###
+### Created : Zhen Li (zhen_li@brown.edu) ###
+### Division of Applied Mathematics, Brown University. ###
+### ###
+### mDPD system setup follows Fig.12 in the publication: ###
+### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
+### "Energy-conserving dissipative particle dynamics with ###
+### temperature-dependent properties". J. Comput. Phys., ###
+### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
+########################################################################
+units lj
+dimension 3
+boundary p p p
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+
+atom_style edpd
+
+region edpd block -10 10 -10 10 -5 5 units box
+create_box 1 edpd
+create_atoms 1 random 16000 276438 NULL
+mass 1 1.0
+set atom * edpd/temp 1.0
+set atom * edpd/cv 1.0E5
+
+pair_style edpd 1.58 9872598
+#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
+pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
+ power 10.54 -3.66 3.44 -4.10 &
+ kappa -0.44 -3.21 5.04 0.00
+
+compute mythermo all temp
+thermo 100
+thermo_modify temp mythermo
+thermo_modify flush yes
+
+velocity all create 1.0 432982 loop local dist gaussian
+
+fix mvv all mvv/edpd 0.5
+fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
+fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
+
+timestep 0.01
+run 500
+reset_timestep 0
+
+compute temp all edpd/temp/atom
+compute ccT all chunk/atom bin/1d y 0.0 1.0
+fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
+
+run 500
diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/meso/mdpd/in.mdpd
index 201b4a340eefd272a3e0e8515a9301b26c9cb769..b0740c822767a59dfa38faacce9cc3c072b1a78d 100644
--- a/examples/USER/meso/mdpd/in.mdpd
+++ b/examples/USER/meso/mdpd/in.mdpd
@@ -1,52 +1,52 @@
-########################################################################
-#### 3D droplet oscilation using many-body DPD simulation ###
-#### ###
-#### Created : Zhen Li (zhen_li@brown.edu) ###
-#### Division of Applied Mathematics, Brown University. ###
-#### ###
-#### mDPD parameters follow the choice of the publication: ###
-#### Z. Li et al. "Three dimensional flow structures in a moving ###
-#### droplet on substrate: a dissipative particle dynamics study" ###
-#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
-########################################################################
-units lj
-dimension 3
-boundary p p p
-neighbor 0.3 bin
-neigh_modify every 1 delay 0 check yes
-
-atom_style mdpd
-
-region mdpd block -25 25 -10 10 -10 10 units box
-create_box 1 mdpd
-
-lattice fcc 6
-region film block -20 20 -7.5 7.5 -2.0 2.0 units box
-create_atoms 1 region film
-
-pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
-pair_coeff 1 1 mdpd/rhosum 0.75
-pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
-mass 1 1.0
-
-compute mythermo all temp
-thermo 100
-thermo_modify temp mythermo
-thermo_modify flush yes
-
-velocity all create 1.0 38497 loop local dist gaussian
-
-fix mvv all mvv/dpd
-
-#dump mydump all atom 100 atom.lammpstrj
-
-#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
-# view 90 90 box no 0 size 600 200
-#dump_modify jpg pad 4
-
-#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
-# view 90 90 box no 0 size 600 200
-#dump_modify avi pad 4
-
-timestep 0.01
-run 4000
+########################################################################
+#### 3D droplet oscilation using many-body DPD simulation ###
+#### ###
+#### Created : Zhen Li (zhen_li@brown.edu) ###
+#### Division of Applied Mathematics, Brown University. ###
+#### ###
+#### mDPD parameters follow the choice of the publication: ###
+#### Z. Li et al. "Three dimensional flow structures in a moving ###
+#### droplet on substrate: a dissipative particle dynamics study" ###
+#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
+########################################################################
+units lj
+dimension 3
+boundary p p p
+neighbor 0.3 bin
+neigh_modify every 1 delay 0 check yes
+
+atom_style mdpd
+
+region mdpd block -25 25 -10 10 -10 10 units box
+create_box 1 mdpd
+
+lattice fcc 6
+region film block -20 20 -7.5 7.5 -2.0 2.0 units box
+create_atoms 1 region film
+
+pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
+pair_coeff 1 1 mdpd/rhosum 0.75
+pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
+mass 1 1.0
+
+compute mythermo all temp
+thermo 100
+thermo_modify temp mythermo
+thermo_modify flush yes
+
+velocity all create 1.0 38497 loop local dist gaussian
+
+fix mvv all mvv/dpd
+
+#dump mydump all atom 100 atom.lammpstrj
+
+#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
+# view 90 90 box no 0 size 600 200
+#dump_modify jpg pad 4
+
+#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
+# view 90 90 box no 0 size 600 200
+#dump_modify avi pad 4
+
+timestep 0.01
+run 4000
diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/meso/tdpd/in.tdpd
index 748a4f50775795c51a26eead61adfaa3a6085477..5107e7a454256a52f2b4b6aed736556775a1e32a 100644
--- a/examples/USER/meso/tdpd/in.tdpd
+++ b/examples/USER/meso/tdpd/in.tdpd
@@ -1,54 +1,54 @@
-########################################################################
-### Pure diffusion with a reaction source term analog of a periodic ###
-### Poiseuille flow problem using transport DPD (tDPD) simulation ###
-### ###
-### Created : Zhen Li (zhen_li@brown.edu) ###
-### Division of Applied Mathematics, Brown University. ###
-### ###
-### tDPD system setup follows Fig.1 in the publication: ###
-### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
-### "Transport dissipative particle dynamics model for mesoscopic ###
-### advection-diffusion-reaction problems. J. Chem. Phys., ###
-### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
-########################################################################
-units lj
-dimension 3
-boundary p p p
-neighbor 0.2 bin
-neigh_modify every 1 delay 0 check yes
-
-atom_style tdpd 2
-
-region tdpd block -10 10 -10 10 -5 5 units box
-create_box 1 tdpd
-create_atoms 1 random 16000 276438 NULL
-mass 1 1.0
-set atom * cc 1 1.0
-set atom * cc 2 1.0
-
-pair_style tdpd 1.0 1.58 9872598
-pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
-
-compute mythermo all temp
-thermo 50
-thermo_modify temp mythermo
-thermo_modify flush yes
-
-velocity all create 1.0 432982 loop local dist gaussian
-
-fix mvv all mvv/tdpd 0.5
-fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
-fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
-fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
-fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
-
-timestep 0.01
-run 500
-reset_timestep 0
-
-compute cc1 all tdpd/cc/atom 1
-compute cc2 all tdpd/cc/atom 2
-compute bin all chunk/atom bin/1d y 0.0 1.0
-fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
-
-run 100
+########################################################################
+### Pure diffusion with a reaction source term analog of a periodic ###
+### Poiseuille flow problem using transport DPD (tDPD) simulation ###
+### ###
+### Created : Zhen Li (zhen_li@brown.edu) ###
+### Division of Applied Mathematics, Brown University. ###
+### ###
+### tDPD system setup follows Fig.1 in the publication: ###
+### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
+### "Transport dissipative particle dynamics model for mesoscopic ###
+### advection-diffusion-reaction problems. J. Chem. Phys., ###
+### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
+########################################################################
+units lj
+dimension 3
+boundary p p p
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+
+atom_style tdpd 2
+
+region tdpd block -10 10 -10 10 -5 5 units box
+create_box 1 tdpd
+create_atoms 1 random 16000 276438 NULL
+mass 1 1.0
+set atom * cc 1 1.0
+set atom * cc 2 1.0
+
+pair_style tdpd 1.0 1.58 9872598
+pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
+
+compute mythermo all temp
+thermo 50
+thermo_modify temp mythermo
+thermo_modify flush yes
+
+velocity all create 1.0 432982 loop local dist gaussian
+
+fix mvv all mvv/tdpd 0.5
+fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
+fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
+fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
+fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
+
+timestep 0.01
+run 500
+reset_timestep 0
+
+compute cc1 all tdpd/cc/atom 1
+compute cc2 all tdpd/cc/atom 2
+compute bin all chunk/atom bin/1d y 0.0 1.0
+fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
+
+run 100
diff --git a/examples/USER/mgpt/log.lammps b/examples/USER/mgpt/log.lammps
deleted file mode 100644
index 9485c36e475718327e8501ba0ba0a622f266e696..0000000000000000000000000000000000000000
--- a/examples/USER/mgpt/log.lammps
+++ /dev/null
@@ -1,78 +0,0 @@
-LAMMPS (23 Oct 2015)
-# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
-# input for relaxed vacancy formation energy at constant pressure
-
-echo screen
-Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
-Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
- 1 by 1 by 1 MPI processor grid
-Created 250 atoms
-Deleted 1 atoms, new total = 249
-Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
-Neighbor list info ...
- 2 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 13.1712
- ghost atom cutoff = 13.1712
- binsize = 6.58562 -> bins = 5 5 5
-Memory usage per processor = 4.66978 Mbytes
-Step Volume Temp PotEng TotEng Press
- 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
- 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
- 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
- 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
- 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
- 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
- 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
- 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
- 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
- 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
- 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
- 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
- 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
- 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
- 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
-Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms
-
-92.4% CPU use with 1 MPI tasks x no OpenMP threads
-
-Minimization stats:
- Stopping criterion = energy tolerance
- Energy initial, next-to-last, final =
- -73.9945109564 -74.0063705487 -74.0063705557
- Force two-norm initial, final = 0.0366227 8.09081e-05
- Force max component initial, final = 0.00730948 8.05242e-06
- Final line search alpha, max atom move = 1 8.05242e-06
- Iterations, force evaluations = 139 139
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43
-Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44
-Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04
-Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.00297 | | | 0.07
-
-Nlocal: 249 ave 249 max 249 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1479 ave 1479 max 1479 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 7936 ave 7936 max 7936 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 15872 ave 15872 max 15872 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15872
-Ave neighs/atom = 63.743
-Neighbor list builds = 4
-Dangerous builds = 0
-number of atoms = 249
-atomic volume (a.u.) = 121.863
-total energy (ry/atom) = -0.594428679162064
-pressure (gpa) = -1.15783109519801
-249 121.863 -148.012741111354 -1.15783109519801
-121.863 -0.594428679162064 -1.15783109519801
-Total wall time: 0:00:04
diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2
index 128f05b489885885fdb68c9953572d71e6d44f76..bb6916fc4847df10707f2712c10955d921878601 100644
--- a/examples/gcmc/in.gcmc.co2
+++ b/examples/gcmc/in.gcmc.co2
@@ -58,21 +58,21 @@ timestep 1.0
# rigid constraints with thermostat
-fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
+fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
-group carbon dynamic all var carbon
-group oxygen dynamic all var oxygen
+group carbon dynamic co2 var carbon
+group oxygen dynamic co2 var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
diff --git a/examples/gcmc/in.gcmc.lj b/examples/gcmc/in.gcmc.lj
index 3fe78efb252d2274a03b812f0bd972db2666952c..a1c7c6eb1002c5bbb7af59e364be39fa9cbc27ef 100644
--- a/examples/gcmc/in.gcmc.lj
+++ b/examples/gcmc/in.gcmc.lj
@@ -29,14 +29,18 @@ create_box 1 box
pair_coeff * * 1.0 1.0
mass * 1.0
+# we recommend setting up a dedicated group for gcmc
+
+group gcmcgroup type 1
+
# gcmc
-fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
# atom count
variable type1 atom "type==1"
-group type1 dynamic all var type1
+group type1 dynamic gcmcgroup var type1
variable n1 equal count(type1)
# averaging
diff --git a/examples/latte/latte.in b/examples/latte/latte.in
index 7df354a742fc8354942ae1a6183e152bfd0c208f..b8b214b78b4847ee4a58c0a03e6f8a94adc78e4b 100644
--- a/examples/latte/latte.in
+++ b/examples/latte/latte.in
@@ -12,7 +12,7 @@ CONTROL{
xControl= 1
BASISTYPE= NONORTHO
COORDSFILE= "./coords.dat"
- PARAMPATH= "/home/user/LATTE/TBparam"
+ PARAMPATH= "./TBparam"
KBT= 0.0
ENTROPYKIND= 1
PPOTON= 1
diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile
index f116508ae5337e86ed07b6570ef1125a4726d897..bb071514474655a9fb36a73fab05635fa9ffdd99 100644
--- a/lib/gpu/Opencl.makefile
+++ b/lib/gpu/Opencl.makefile
@@ -65,7 +65,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
$(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
$(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
$(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
- $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o
+ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
+ $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o
KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
$(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \
@@ -93,7 +94,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
$(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h \
$(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \
$(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \
- $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h
+ $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \
+ $(OBJ_DIR)/ufm_cl.h
OCL_EXECS = $(BIN_DIR)/ocl_get_devices
@@ -577,6 +579,15 @@ $(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/
$(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h
$(OCL) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR)
+$(OBJ_DIR)/ufm_cl.h: lal_ufm.cu $(PRE1_H)
+ $(BSH) ./geryon/file_to_cstr.sh ufm $(PRE1_H) lal_ufm.cu $(OBJ_DIR)/ufm_cl.h;
+
+$(OBJ_DIR)/lal_ufm.o: $(ALL_H) lal_ufm.h lal_ufm.cpp $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/lal_base_atomic.o
+ $(OCL) -o $@ -c lal_ufm.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_ufm_ext.o: $(ALL_H) lal_ufm.h lal_ufm_ext.cpp lal_base_atomic.h
+ $(OCL) -o $@ -c lal_ufm_ext.cpp -I$(OBJ_DIR)
+
$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp
$(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK)
diff --git a/python/lammps.py b/python/lammps.py
index 0492876476ea7d2ce50a709eb498ec819beac0ae..c895037c00d97e16116010157fb922dde58fe3ab 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -406,7 +406,7 @@ class lammps(object):
# returned data is a 1d vector - doc how it is ordered?
# NOTE: how could we insure are converting to correct Python type
# e.g. for Python list or NumPy, etc
- # ditto for extact_atom() above
+ # ditto for extract_atom() above
def gather_atoms(self,name,type,count):
if name: name = name.encode()
diff --git a/src/.gitignore b/src/.gitignore
index e193c622dfb0cfab0a8c502e21703d489325f9de..649ca414ff3b13a982236c70d1be047e8ff6ad2b 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -15,6 +15,8 @@
/*_kokkos.cpp
/*_omp.h
/*_omp.cpp
+/*_opt.h
+/*_opt.cpp
/*_tally.h
/*_tally.cpp
/*_rx.h
@@ -695,16 +697,10 @@
/pair_dsmc.h
/pair_eam.cpp
/pair_eam.h
-/pair_eam_opt.cpp
-/pair_eam_opt.h
/pair_eam_alloy.cpp
/pair_eam_alloy.h
-/pair_eam_alloy_opt.cpp
-/pair_eam_alloy_opt.h
/pair_eam_fs.cpp
/pair_eam_fs.h
-/pair_eam_fs_opt.cpp
-/pair_eam_fs_opt.h
/pair_edip.cpp
/pair_edip.h
/pair_edip_multi.cpp
@@ -748,8 +744,6 @@
/pair_lj_charmm_coul_charmm_implicit.h
/pair_lj_charmm_coul_long.cpp
/pair_lj_charmm_coul_long.h
-/pair_lj_charmm_coul_long_opt.cpp
-/pair_lj_charmm_coul_long_opt.h
/pair_lj_charmm_coul_long_soft.cpp
/pair_lj_charmm_coul_long_soft.h
/pair_lj_charmm_coul_msm.cpp
@@ -772,8 +766,6 @@
/pair_lj_cut_tip4p_cut.h
/pair_lj_cut_coul_long.cpp
/pair_lj_cut_coul_long.h
-/pair_lj_cut_coul_long_opt.cpp
-/pair_lj_cut_coul_long_opt.h
/pair_lj_cut_coul_long_soft.cpp
/pair_lj_cut_coul_long_soft.h
/pair_lj_cut_coul_msm.cpp
@@ -788,20 +780,14 @@
/pair_lj_cut_soft.h
/pair_lj_cut_tip4p_long.cpp
/pair_lj_cut_tip4p_long.h
-/pair_lj_cut_tip4p_long_opt.cpp
-/pair_lj_cut_tip4p_long_opt.h
/pair_lj_cut_tip4p_long_soft.cpp
/pair_lj_cut_tip4p_long_soft.h
/pair_lj_long_coul_long.cpp
/pair_lj_long_coul_long.h
-/pair_lj_long_coul_long_opt.cpp
-/pair_lj_long_coul_long_opt.h
/pair_lj_long_dipole_long.cpp
/pair_lj_long_dipole_long.h
/pair_lj_long_tip4p_long.cpp
/pair_lj_long_tip4p_long.h
-/pair_lj_cut_opt.cpp
-/pair_lj_cut_opt.h
/pair_lj_cut_tgpu.cpp
/pair_lj_cut_tgpu.h
/pair_lj_sdk.cpp
@@ -826,8 +812,6 @@
/pair_meam_spline.h
/pair_meam_sw_spline.cpp
/pair_meam_sw_spline.h
-/pair_morse_opt.cpp
-/pair_morse_opt.h
/pair_morse_soft.cpp
/pair_morse_soft.h
/pair_nb3b_harmonic.cpp
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index 5fa03a098925430d50f5dd09bc59612398a9d759..b2b107284ec26109843db5092bf1dc9594acee8e 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -119,7 +119,7 @@ void VerletKokkos::setup(int flag)
atomKK->modified(Host,ALL_MASK);
- neighbor->build();
+ neighbor->build(1);
neighbor->ncalls = 0;
// compute all forces
@@ -222,7 +222,7 @@ void VerletKokkos::setup_minimal(int flag)
atomKK->modified(Host,ALL_MASK);
- neighbor->build();
+ neighbor->build(1);
neighbor->ncalls = 0;
}
@@ -378,7 +378,7 @@ void VerletKokkos::run(int n)
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
diff --git a/src/KOKKOS/verlet_kokkos.h b/src/KOKKOS/verlet_kokkos.h
index 7b140b6f81ae40bdb393534c7ce29e0f564bc5f2..1e36b1cf6eb718c5296eb9cde905c066f9f3e606 100644
--- a/src/KOKKOS/verlet_kokkos.h
+++ b/src/KOKKOS/verlet_kokkos.h
@@ -31,7 +31,7 @@ class VerletKokkos : public Verlet {
public:
VerletKokkos(class LAMMPS *, int, char **);
~VerletKokkos() {}
- void setup(int flag=1);
+ void setup(int);
void setup_minimal(int);
void run(int);
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index f74b05624f8f62ba4cfc6d1bf3dacdcb33149ecb..4594f26f8f8c182901ed564895e5814d77cb5e06 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -38,7 +38,8 @@ extern "C" {
void latte(int *, int *, double *, int *, int *,
double *, double *, double *, double *,
double *, double *, double *, int*,
- double *, double *, double *, double * );
+ double *, double *, double *, double *, bool *);
+ int latte_abiversion();
}
#define INVOKED_PERATOM 8
@@ -54,6 +55,9 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
if (comm->nprocs != 1)
error->all(FLERR,"Fix latte currently runs only in serial");
+ if (20180207 != latte_abiversion())
+ error->all(FLERR,"LAMMPS is linked against incompatible LATTE library");
+
if (narg != 4) error->all(FLERR,"Illegal fix latte command");
scalar_flag = 1;
@@ -267,7 +271,7 @@ void FixLatte::post_force(int vflag)
flags[1] = coulombflag; // 1 for LAMMPS computes Coulombics, 0 for LATTE
flags[2] = eflag_atom; // 1 to return per-atom energies, 0 for no
flags[3] = vflag_global && thermo_virial; // 1 to return global/per-atom
- flags[4] = vflag_atom && thermo_virial; // virial, 0 for no
+ flags[4] = vflag_atom && thermo_virial; // virial, 0 for no
flags[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no
// setup LATTE arguments
@@ -279,16 +283,17 @@ void FixLatte::post_force(int vflag)
double *mass = &atom->mass[1];
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
-
double *forces;
+ bool latteerror = 0;
if (coulomb) forces = &flatte[0][0];
else forces = &atom->f[0][0];
-
int maxiter = -1;
-
+
latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy,
- &domain->xz,&domain->yz,
- forces,&maxiter,&latte_energy,&atom->v[0][0],&update->dt,virial);
+ &domain->xz,&domain->yz,forces,&maxiter,&latte_energy,
+ &atom->v[0][0],&update->dt,virial,&latteerror);
+
+ if (latteerror) error->all(FLERR,"Internal LATTE problem");
// sum LATTE forces to LAMMPS forces
// e.g. LAMMPS may compute Coulombics at some point
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 80bebefec027304bcf020a2cb5d989d523d7ba89..6500707bf3f1812ef3e84b0a46dd5d8c45e4a669 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -316,7 +316,7 @@ void FixAtomSwap::pre_exchange()
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
energy_stored = energy_full();
@@ -366,7 +366,7 @@ int FixAtomSwap::attempt_semi_grand()
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
} else {
comm->forward_comm_fix(this);
}
@@ -408,7 +408,7 @@ int FixAtomSwap::attempt_semi_grand()
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
} else {
comm->forward_comm_fix(this);
}
@@ -447,7 +447,7 @@ int FixAtomSwap::attempt_swap()
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
} else {
comm->forward_comm_fix(this);
}
@@ -489,7 +489,7 @@ int FixAtomSwap::attempt_swap()
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
} else {
comm->forward_comm_fix(this);
}
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index a50ca0fd21e7004ed27fa021deb172536fcbe33a..02300844907b16767986019acc77af28f2edc1c3 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -72,7 +72,8 @@ enum{MOVEATOM,MOVEMOL}; // movemode
FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),
- grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), random_equal(NULL), random_unequal(NULL),
+ grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), molq(NULL), molimage(NULL),
+ random_equal(NULL), random_unequal(NULL),
fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
@@ -199,8 +200,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (exchmode == EXCHATOM) natoms_per_molecule = 1;
else natoms_per_molecule = onemols[imol]->natoms;
- nmaxmolcoords = natoms_per_molecule;
- memory->create(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
+ nmaxmolatoms = natoms_per_molecule;
+ grow_molecule_arrays(nmaxmolatoms);
// compute the number of MC cycles that occur nevery timesteps
@@ -513,7 +514,7 @@ void FixGCMC::init()
"Fix gcmc cannot exchange individual atoms belonging to a molecule");
}
- // if molecules are exchanged are moves, check for unset mol IDs
+ // if molecules are exchanged or moved, check for unset mol IDs
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
tagint *molecule = atom->molecule;
@@ -683,6 +684,12 @@ void FixGCMC::init()
imagezero = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ // warning if group id is "all"
+
+ if (groupbit & 1)
+ error->warning(FLERR, "Fix gcmc is being applied "
+ "to the default group all");
+
// construct group bitmask for all new atoms
// aggregated over all group keywords
@@ -1153,10 +1160,8 @@ void FixGCMC::attempt_molecule_rotation()
}
}
- if (nmolcoords > nmaxmolcoords) {
- nmaxmolcoords = nmolcoords;
- molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
- }
+ if (nmolcoords > nmaxmolatoms)
+ grow_molecule_arrays(nmolcoords);
double com[3];
com[0] = com[1] = com[2] = 0.0;
@@ -1816,10 +1821,8 @@ void FixGCMC::attempt_molecule_rotation_full()
}
}
- if (nmolcoords > nmaxmolcoords) {
- nmaxmolcoords = nmolcoords;
- molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
- }
+ if (nmolcoords > nmaxmolatoms)
+ grow_molecule_arrays(nmolcoords);
double com[3];
com[0] = com[1] = com[2] = 0.0;
@@ -1844,14 +1847,14 @@ void FixGCMC::attempt_molecule_rotation_full()
double **x = atom->x;
imageint *image = atom->image;
- imageint image_orig[natoms_per_molecule];
+
int n = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & molecule_group_bit) {
molcoords[n][0] = x[i][0];
molcoords[n][1] = x[i][1];
molcoords[n][2] = x[i][2];
- image_orig[n] = image[i];
+ molimage[n] = image[i];
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
@@ -1884,7 +1887,7 @@ void FixGCMC::attempt_molecule_rotation_full()
x[i][0] = molcoords[n][0];
x[i][1] = molcoords[n][1];
x[i][2] = molcoords[n][2];
- image[i] = image_orig[n];
+ image[i] = molimage[n];
n++;
}
}
@@ -1906,8 +1909,17 @@ void FixGCMC::attempt_molecule_deletion_full()
double energy_before = energy_stored;
+ // check nmolq, grow arrays if necessary
+
+ int nmolq = 0;
+ for (int i = 0; i < atom->nlocal; i++)
+ if (atom->molecule[i] == deletion_molecule)
+ if (atom->q_flag) nmolq++;
+
+ if (nmolq > nmaxmolatoms)
+ grow_molecule_arrays(nmolq);
+
int m = 0;
- double q_tmp[natoms_per_molecule];
int tmpmask[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
@@ -1915,7 +1927,7 @@ void FixGCMC::attempt_molecule_deletion_full()
atom->mask[i] = exclusion_group_bit;
toggle_intramolecular(i);
if (atom->q_flag) {
- q_tmp[m] = atom->q[i];
+ molq[m] = atom->q[i];
m++;
atom->q[i] = 0.0;
}
@@ -1948,7 +1960,7 @@ void FixGCMC::attempt_molecule_deletion_full()
atom->mask[i] = tmpmask[i];
toggle_intramolecular(i);
if (atom->q_flag) {
- atom->q[i] = q_tmp[m];
+ atom->q[i] = molq[m];
m++;
}
}
@@ -2238,7 +2250,7 @@ double FixGCMC::energy_full()
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
int eflag = 1;
int vflag = 0;
@@ -2521,3 +2533,10 @@ void FixGCMC::restart(char *buf)
next_reneighbor = static_cast<int> (list[n++]);
}
+
+void FixGCMC::grow_molecule_arrays(int nmolatoms) {
+ nmaxmolatoms = nmolatoms;
+ molcoords = memory->grow(molcoords,nmaxmolatoms,3,"gcmc:molcoords");
+ molq = memory->grow(molq,nmaxmolatoms,"gcmc:molq");
+ molimage = memory->grow(molimage,nmaxmolatoms,"gcmc:molimage");
+}
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index fc6021efea32fdd6b01e7f9161577ec318ff4a96..77dda17fdaeccbf5cd16f63b3e86e83baa7c51da 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -57,7 +57,8 @@ class FixGCMC : public Fix {
double memory_usage();
void write_restart(FILE *);
void restart(char *);
-
+ void grow_molecule_arrays(int);
+
private:
int molecule_group,molecule_group_bit;
int molecule_group_inversebit;
@@ -78,7 +79,7 @@ class FixGCMC : public Fix {
bool full_flag; // true if doing full system energy calculations
int natoms_per_molecule; // number of atoms in each inserted molecule
- int nmaxmolcoords; // number of atoms allocated for molcoords
+ int nmaxmolatoms; // number of atoms allocated for molecule arrays
int groupbitall; // group bitmask for inserted atoms
int ngroups; // number of group-ids for inserted atoms
@@ -114,6 +115,8 @@ class FixGCMC : public Fix {
int *local_gas_list;
double **cutsq;
double **molcoords;
+ double *molq;
+ imageint *molimage;
imageint imagezero;
double overlap_cutoffsq; // square distance cutoff for overlap
int overlap_flag;
@@ -224,6 +227,12 @@ W: Energy of old configuration in fix gcmc is > MAXENERGYTEST.
This probably means that a pair of atoms are closer than the
overlap cutoff distance for keyword overlap_cutoff.
+W: Fix gcmc is being applied to the default group all
+
+This is allowed, but it will result in Monte Carlo moves
+being performed on all the atoms in the system, which is
+often not what is intended.
+
E: Invalid atom type in fix gcmc command
The atom type specified in the gcmc command does not exist.
diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h
index ac318aa58c6e6e477ecea7e1d08f41483cfa66ed..605374c47fc7172f42dad2a89137628e2b8bc236 100644
--- a/src/MISC/xdr_compat.h
+++ b/src/MISC/xdr_compat.h
@@ -60,7 +60,7 @@ extern "C" {
typedef int bool_t;
-#if defined(__MINGW32__)
+#if defined(__MINGW32__) || defined(__APPLE__)
typedef char * caddr_t;
typedef unsigned int u_int;
#endif
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 757eae5dd2f32093aefdd0e3f5c0b989b97ebeb9..b9dfbdae190818f9e0895e17cdf46944fa5dab22 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -362,6 +362,7 @@ int FixQEq::CG( double *b, double *x )
i = ilist[ii];
if (atom->mask[i] & groupbit)
d[i] = r[i] * Hdia_inv[i];
+ else d[i] = 0.0;
}
b_norm = parallel_norm( b, inum );
@@ -594,6 +595,7 @@ double FixQEq::parallel_norm( double *v, int n )
ilist = list->ilist;
my_sum = 0.0;
+ norm_sqr = 0.0;
for( ii = 0; ii < n; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit)
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index 98e55398728c06caf536ee925b988f359376d84a..33f834a14069b42d4fa56379c35db41a2e102379 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -425,10 +425,14 @@ void FixNEB::min_post_force(int vflag)
tangent[i][0] = vmax*delxn + vmin*delxp;
tangent[i][1] = vmax*delyn + vmin*delyp;
tangent[i][2] = vmax*delzn + vmin*delzp;
- } else {
+ } else if (vnext < vprev) {
tangent[i][0] = vmin*delxn + vmax*delxp;
tangent[i][1] = vmin*delyn + vmax*delyp;
tangent[i][2] = vmin*delzn + vmax*delzp;
+ } else { // vnext == vprev, e.g. for potentials that do not compute an energy
+ tangent[i][0] = delxn + delxp;
+ tangent[i][1] = delyn + delyp;
+ tangent[i][2] = delzn + delzp;
}
}
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 14eeac8d664551927278454f577de998a7bdc4a0..f7d369cee6a4b162a5fdecc040310f5f60c492b5 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -293,7 +293,7 @@ void PRD::command(int narg, char **arg)
update->whichflag = 1;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
if (temp_flag == 0) {
if (universe->iworld == 0) temp_dephase = temperature->compute_scalar();
@@ -390,7 +390,7 @@ void PRD::command(int narg, char **arg)
update->whichflag = 1;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
timer->barrier_start();
@@ -545,7 +545,7 @@ void PRD::dynamics(int nsteps, double &time_category)
update->nsteps = nsteps;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
// this may be needed if don't do full init
//modify->addstep_compute_all(update->ntimestep);
bigint ncalls = neighbor->ncalls;
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 347cd3ba67c0927740086a879d2de5f750cf3faf..958a57e4e8936e895621fd4ec6fb5cf89baf153e 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -264,7 +264,7 @@ void TAD::command(int narg, char **arg)
update->whichflag = 1;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
// main loop: look for events until out of time
// (1) dynamics, store state, quench, check event, restore state
@@ -342,7 +342,7 @@ void TAD::command(int narg, char **arg)
update->whichflag = 1;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
// write restart file of hot coords
@@ -448,7 +448,7 @@ void TAD::dynamics()
update->nsteps = t_event;
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
// this may be needed if don't do full init
//modify->addstep_compute_all(update->ntimestep);
int ncalls = neighbor->ncalls;
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 667f2893c6da1c43828f78c561a0a5d49338b308..d7e8c981bb51a729595aeee17ae8c2c4b43fd71d 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -212,7 +212,7 @@ void Temper::command(int narg, char **arg)
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
- update->integrate->setup();
+ update->integrate->setup(1);
if (me_universe == 0) {
if (universe->uscreen) {
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index 4572170f34f6132fa4ca6ef1b081147142a8d011..e47965d1c3c02a28f00351c5a8139caf4514915c 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -239,13 +239,13 @@ void VerletSplit::init()
servant partition only sets up KSpace calculation
------------------------------------------------------------------------- */
-void VerletSplit::setup()
+void VerletSplit::setup(int flag)
{
if (comm->me == 0 && screen)
fprintf(screen,"Setting up Verlet/split run ...\n");
if (!master) force->kspace->setup();
- else Verlet::setup();
+ else Verlet::setup(flag);
}
/* ----------------------------------------------------------------------
@@ -344,7 +344,7 @@ void VerletSplit::run(int n)
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
if (n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
}
diff --git a/src/REPLICA/verlet_split.h b/src/REPLICA/verlet_split.h
index 2d25131df30b5c289a4983a317f98f79ec7b336b..b3ee87e580bbfc47e7585c05ce0d9195cc3d6af5 100644
--- a/src/REPLICA/verlet_split.h
+++ b/src/REPLICA/verlet_split.h
@@ -29,7 +29,7 @@ class VerletSplit : public Verlet {
VerletSplit(class LAMMPS *, int, char **);
~VerletSplit();
void init();
- void setup();
+ void setup(int);
void setup_minimal(int);
void run(int);
bigint memory_usage();
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 39b7ba22246065e6616cac705c48e87fc794a02a..2b7a69503acd37062d60094399f40da30bd23831 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -529,7 +529,7 @@ while (ct-- > 0) {
void FixShardlow::initial_integrate(int vflag)
{
- int i,ii,inum;
+ int ii;
int *ilist;
int nlocal = atom->nlocal;
@@ -592,9 +592,7 @@ void FixShardlow::initial_integrate(int vflag)
// Allocate memory for v_t0 to hold the initial velocities for the ghosts
v_t0 = (double (*)[3]) memory->smalloc(sizeof(double)*3*nghost, "FixShardlow:v_t0");
- inum = list->inum;
ilist = list->ilist;
-
dtsqrt = sqrt(update->dt);
// process neighbors in the local AIR
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
index ce50f7603adb0a757bbf9e03d0f31830e0272bd7..ba90ebc465228992237b008e6e28e54a3bbd44c4 100644
--- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
@@ -85,8 +85,6 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int nlocal = atom->nlocal;
- if (includegroup) nlocal = atom->nfirst;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
@@ -168,7 +166,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
for (int subphase = 0; subphase < 4; subphase++) {
int s_ybin = ybin + ((subphase & 0x2) ? ns_ssa->sy : 0);
int s_xbin = xbin + ((subphase & 0x1) ? ns_ssa->sx : 0);
- int ibin, ct;
+ int ibin;
if ((s_ybin < lbinylo) || (s_ybin >= lbinyhi)) continue;
if ((s_xbin < lbinxlo) || (s_xbin >= lbinxhi)) continue;
diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp
index 9ff5f8517608fa74c7c9916824aa723247ef3fa6..1b9c305e9c69377906b0346de8b6803c37b307b9 100644
--- a/src/USER-INTEL/verlet_lrt_intel.cpp
+++ b/src/USER-INTEL/verlet_lrt_intel.cpp
@@ -142,7 +142,7 @@ void VerletLRTIntel::setup(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
neighbor->ncalls = 0;
// compute all forces
@@ -276,7 +276,7 @@ void VerletLRTIntel::run(int n)
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/USER-INTEL/verlet_lrt_intel.h
index 0d7154ff643ee7a71af39057b13668345939ce1d..7380cc6376b3c649351579ecbc0a563f6a85cf99 100644
--- a/src/USER-INTEL/verlet_lrt_intel.h
+++ b/src/USER-INTEL/verlet_lrt_intel.h
@@ -41,7 +41,7 @@ class VerletLRTIntel : public Verlet {
VerletLRTIntel(class LAMMPS *, int, char **);
virtual ~VerletLRTIntel();
virtual void init();
- virtual void setup(int flag = 1);
+ virtual void setup(int flag);
virtual void run(int);
protected:
diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp
index 0a4d302c36f23f1eb95af141ec92f9a070f562d7..0d2350a645c260f8d0e81abad6c55263edf6bf15 100644
--- a/src/USER-MESO/atom_vec_mdpd.cpp
+++ b/src/USER-MESO/atom_vec_mdpd.cpp
@@ -43,9 +43,9 @@ AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp)
size_reverse = 3 + 1; // 3 + drho
size_border = 6 + 4; // 6 + rho + vest[3]
size_velocity = 3;
- size_data_atom = 5;
+ size_data_atom = 6;
size_data_vel = 4;
- xcol_data = 3;
+ xcol_data = 4;
atom->rho_flag = 1;
atom->vest_flag = 1;
@@ -817,7 +817,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) {
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
- rho[nlocal] = 0.0;
+ rho[nlocal] = atof(values[2]);
drho[nlocal] = 0.0;
atom->nlocal++;
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index 77a67273f6389c3a3a9e68220201223cff8dc925..299f453ea7c308c28d489662c00a8d716da3c881 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -61,6 +61,9 @@ int FixMvvDPD::setmask()
void FixMvvDPD::init()
{
+ if (!atom->vest_flag)
+ error->all(FLERR,"Fix mvv/dpd requires atom attribute vest");
+
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp
index bf78ea5af705745e59e61c429c50253efd94e871..ba72304ddb61ac34a3f4561c5786b48aae340f67 100644
--- a/src/USER-MESO/pair_mdpd.cpp
+++ b/src/USER-MESO/pair_mdpd.cpp
@@ -282,6 +282,9 @@ void PairMDPD::init_style()
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair mdpd requires ghost atoms store velocity");
+ if (!atom->rho_flag)
+ error->all(FLERR,"Pair style mdpd requires atom attribute rho");
+
// if newton off, forces between atoms ij will be double computed
// using different random numbers
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index 9c4d6f804f8df883ebbf13c8a7c2c5903e11119d..d2a4ad33d84c3860032348e4651d93ae50481125 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -62,7 +62,11 @@ PairMDPDRhoSum::~PairMDPDRhoSum() {
init specific to this pair style
------------------------------------------------------------------------- */
-void PairMDPDRhoSum::init_style() {
+void PairMDPDRhoSum::init_style()
+{
+ if (!atom->rho_flag)
+ error->all(FLERR,"Pair style mdpd/rhosum requires atom attribute rho");
+
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 1f2bd4eb6c7cdd9bde32707523ed80ebc5656af2..42904d2b5a168a5148fe4bd74fad73b436f5a5d6 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -315,13 +315,17 @@ void PairTDPD::coeff(int narg, char **arg)
void PairTDPD::init_style()
{
if (comm->ghost_velocity == 0)
- error->all(FLERR,"Pair tdpd requires ghost atoms store velocity");
+ error->all(FLERR,"Pair style tdpd requires ghost atoms store velocity");
+
+ if (!atom->tdpd_flag)
+ error->all(FLERR,"Pair style tdpd requires atom properties cc/cc_flux");
// if newton off, forces between atoms ij will be double computed
// using different random numbers
- if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR,
- "Pair tdpd needs newton pair on for momentum conservation");
+ if (force->newton_pair == 0 && comm->me == 0)
+ error->warning(FLERR,"Pair tdpd needs newton pair on "
+ "for momentum conservation");
neighbor->request(this,instance_me);
}
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index e1e5f579b875c31f16c70c3f55ba3d44a3f14494..aeaf2f78ba8500660cf758261a4b6de92709f90d 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -304,7 +304,7 @@ void FixSRP::setup_pre_force(int zz)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
neighbor->ncalls = 0;
// new atom counts
diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp
index 6ce7da8d6adea2267ebbb87a92469cfe7367f41f..9e5a4c5c3b95aed6cec87ea62e88d000874d9cc8 100644
--- a/src/USER-MISC/temper_grem.cpp
+++ b/src/USER-MISC/temper_grem.cpp
@@ -214,7 +214,7 @@ void TemperGrem::command(int narg, char **arg)
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
- update->integrate->setup();
+ update->integrate->setup(1);
if (me_universe == 0) {
if (universe->uscreen) {
diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp
index 572a52b1a921c347d4d70469f9664d7831ed404f..60f9313fdd7a192b1ae59b6720204f9c13cebadf 100644
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@@ -101,9 +101,9 @@ void TemperNPT::command(int narg, char **arg)
// change the volume. This currently only applies to fix npt and
// fix rigid/npt variants
- if ((strncmp(modify->fix[whichfix]->style,"npt",3) == 0)
- || (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) == 0))
- error->universe_all(FLERR,"Tempering temperature fix is not supported");
+ if ((strncmp(modify->fix[whichfix]->style,"npt",3) != 0)
+ && (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) != 0))
+ error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
// setup for long tempering run
@@ -190,7 +190,7 @@ void TemperNPT::command(int narg, char **arg)
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
- update->integrate->setup();
+ update->integrate->setup(1);
if (me_universe == 0) {
if (universe->uscreen) {
diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp
index 37f343736d6ae05f34695304e9d1219e45a6121c..9c0c15f1ee3d6524cfe1c01b3aaa3cf155c12c5d 100644
--- a/src/USER-MOLFILE/molfile_interface.cpp
+++ b/src/USER-MOLFILE/molfile_interface.cpp
@@ -107,7 +107,7 @@ extern "C" {
* J. Phys. Chem., 68, 441 - 452, 1964,
* except the value for H, which is taken from R.S. Rowland & R. Taylor,
* J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
- * either of these publications have RvdW = 2.00 Å.
+ * either of these publications have RvdW = 2.00 \AA.
* The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
* Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.
*/
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index 6a1cb46ea6272d9c312c8c555b74fdbf2eebdbd7..fc101a33d21ce88b683df8835b5d083af287cbd5 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -49,7 +49,7 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
#endif
NPAIR_OMP_SETUP(nlocal);
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
@@ -58,7 +58,6 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index d8e1e6da449c9e04698dc79df919a802e907cec9..1f0dca79ac1b072b05176254577b3954bcb390e3 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -48,14 +48,13 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
#endif
NPAIR_OMP_SETUP(nlocal);
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
index 3c7b6b118f5f9a4da6f324acb9b217097bf69605..1615effad3864afbec6ee9633580bd754c44a834 100644
--- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -51,14 +51,13 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
#endif
NPAIR_OMP_SETUP(nlocal);
- int i,j,m,n,nn;
+ int i,j,n;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
index 37a4181af73dd823a9a2eea1475d3c33eb06b15a..e5de57aa5112698f7bc069914eef8d5d9256401d 100644
--- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -52,7 +52,7 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
#endif
NPAIR_OMP_SETUP(nlocal);
- int i,j,m,n,nn,itag,jtag;
+ int i,j,n,itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f5dc03e36828c60e1e68c509be24ee4d5c679ee2
--- /dev/null
+++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
@@ -0,0 +1,204 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ This software is distributed under the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include "pair_lj_cut_coul_wolf_omp.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+
+#include "suffix.h"
+#include "math_const.h"
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+PairLJCutCoulWolfOMP::PairLJCutCoulWolfOMP(LAMMPS *lmp) :
+ PairLJCutCoulWolf(lmp), ThrOMP(lmp, THR_PAIR)
+{
+ suffix_flag |= Suffix::OMP;
+ respa_enable = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutCoulWolfOMP::compute(int eflag, int vflag)
+{
+ if (eflag || vflag) {
+ ev_setup(eflag,vflag);
+ } else evflag = vflag_fdotr = 0;
+
+ const int nall = atom->nlocal + atom->nghost;
+ const int nthreads = comm->nthreads;
+ const int inum = list->inum;
+
+#if defined(_OPENMP)
+#pragma omp parallel default(none) shared(eflag,vflag)
+#endif
+ {
+ int ifrom, ito, tid;
+
+ loop_setup_thr(ifrom, ito, tid, inum, nthreads);
+ ThrData *thr = fix->get_thr(tid);
+ thr->timer(Timer::START);
+ ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+
+ if (evflag) {
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
+ }
+ } else {
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
+ }
+
+ thr->timer(Timer::PAIR);
+ reduce_thr(this, eflag, vflag, thr);
+ } // end of omp parallel region
+}
+
+/* ---------------------------------------------------------------------- */
+
+template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
+void PairLJCutCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
+{
+ int i,j,ii,jj,jnum,itype,jtype;
+ double qitmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+ double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
+ double prefactor,erfcc,erfcd,v_sh,dvdrr,e_self,qisq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = ecoul = 0.0;
+
+ const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
+ dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
+ const double * _noalias const q = atom->q;
+ const int * _noalias const type = atom->type;
+ const int nlocal = atom->nlocal;
+ const double * _noalias const special_coul = force->special_coul;
+ const double * _noalias const special_lj = force->special_lj;
+ const double qqrd2e = force->qqrd2e;
+ double fxtmp,fytmp,fztmp;
+
+ // self and shifted Coulombic energy
+
+ e_self = v_sh = 0.0;
+ const double e_shift = erfc(alf*cut_coul)/cut_coul;
+ const double f_shift = -(e_shift+ 2.0*alf/MY_PIS
+ * exp(-alf*alf*cut_coul*cut_coul)) / cut_coul;
+
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = iifrom; ii < iito; ++ii) {
+
+ i = ilist[ii];
+ qitmp = q[i];
+ xtmp = x[i].x;
+ ytmp = x[i].y;
+ ztmp = x[i].z;
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ fxtmp=fytmp=fztmp=0.0;
+
+ if (EFLAG) {
+ e_self = -(e_shift/2.0 + alf/MY_PIS) * qitmp*qitmp*qqrd2e;
+ ev_tally_thr(this,i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0,thr);
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j].x;
+ dely = ytmp - x[j].y;
+ delz = ztmp - x[j].z;
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ prefactor = qqrd2e*qitmp*q[j]/r;
+ erfcc = erfc(alf*r);
+ erfcd = exp(-alf*alf*r*r);
+ v_sh = (erfcc - e_shift*r) * prefactor;
+ dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
+ forcecoul = dvdrr*rsq*prefactor;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j].x -= delx*fpair;
+ f[j].y -= dely*fpair;
+ f[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
+ }
+ }
+ f[i].x += fxtmp;
+ f[i].y += fytmp;
+ f[i].z += fztmp;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJCutCoulWolfOMP::memory_usage()
+{
+ double bytes = memory_usage_thr();
+ bytes += PairLJCutCoulWolf::memory_usage();
+
+ return bytes;
+}
diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h
new file mode 100644
index 0000000000000000000000000000000000000000..4e56808c7bdb02350a8bce7a68faa5f42f98f8a5
--- /dev/null
+++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h
@@ -0,0 +1,48 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/cut/coul/wolf/omp,PairLJCutCoulWolfOMP)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CUT_COUL_WOLF_OMP_H
+#define LMP_PAIR_LJ_CUT_COUL_WOLF_OMP_H
+
+#include "pair_lj_cut_coul_wolf.h"
+#include "thr_omp.h"
+
+namespace LAMMPS_NS {
+
+class PairLJCutCoulWolfOMP : public PairLJCutCoulWolf, public ThrOMP {
+
+ public:
+ PairLJCutCoulWolfOMP(class LAMMPS *);
+
+ virtual void compute(int, int);
+ virtual double memory_usage();
+
+ private:
+ template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
+ void eval(int ifrom, int ito, ThrData * const thr);
+};
+
+}
+
+#endif
+#endif
diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp
index aa4aa65a4fcefec8bc143367d63347306c1c3bc6..e596caab81729d5f0bbc0c4c7ec12d15f920fe05 100644
--- a/src/USER-OMP/respa_omp.cpp
+++ b/src/USER-OMP/respa_omp.cpp
@@ -67,24 +67,26 @@ void RespaOMP::init()
setup before run
------------------------------------------------------------------------- */
-void RespaOMP::setup()
+void RespaOMP::setup(int flag)
{
if (comm->me == 0 && screen) {
fprintf(screen,"Setting up r-RESPA/omp run ...\n");
- fprintf(screen," Unit style : %s\n", update->unit_style);
- fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep);
- fprintf(screen," Time steps :");
- for (int ilevel=0; ilevel < nlevels; ++ilevel)
- fprintf(screen," %d:%g",ilevel+1, step[ilevel]);
- fprintf(screen,"\n r-RESPA fixes :");
- for (int l=0; l < modify->n_post_force_respa; ++l) {
- Fix *f = modify->fix[modify->list_post_force_respa[l]];
- if (f->respa_level >= 0)
- fprintf(screen," %d:%s[%s]",
- MIN(f->respa_level+1,nlevels),f->style,f->id);
+ if (flag) {
+ fprintf(screen," Unit style : %s\n", update->unit_style);
+ fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep);
+ fprintf(screen," Time steps :");
+ for (int ilevel=0; ilevel < nlevels; ++ilevel)
+ fprintf(screen," %d:%g",ilevel+1, step[ilevel]);
+ fprintf(screen,"\n r-RESPA fixes :");
+ for (int l=0; l < modify->n_post_force_respa; ++l) {
+ Fix *f = modify->fix[modify->list_post_force_respa[l]];
+ if (f->respa_level >= 0)
+ fprintf(screen," %d:%s[%s]",
+ MIN(f->respa_level+1,nlevels),f->style,f->id);
+ }
+ fprintf(screen,"\n");
+ timer->print_timeout(screen);
}
- fprintf(screen,"\n");
- timer->print_timeout(screen);
}
update->setupflag = 1;
@@ -107,7 +109,7 @@ void RespaOMP::setup()
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
@@ -200,7 +202,7 @@ void RespaOMP::setup_minimal(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
}
@@ -311,7 +313,7 @@ void RespaOMP::recurse(int ilevel)
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
if (modify->n_post_neighbor) {
modify->post_neighbor();
diff --git a/src/USER-OMP/respa_omp.h b/src/USER-OMP/respa_omp.h
index 89ddbe78af8b42acb5260cdf79e3499a18514afb..dc01e3dc5bc9d09db88e650ea453509bdfd92b77 100644
--- a/src/USER-OMP/respa_omp.h
+++ b/src/USER-OMP/respa_omp.h
@@ -30,7 +30,7 @@ class RespaOMP : public Respa, public ThrOMP {
RespaOMP(class LAMMPS *, int, char **);
virtual ~RespaOMP() {}
virtual void init();
- virtual void setup();
+ virtual void setup(int);
virtual void setup_minimal(int);
protected:
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index d6ddc9c72d4f0a7c0ace6faee3eac27f05b2dd8f..8dac846017f3253f37be8332db914be9b321d315 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -775,9 +775,9 @@ void PairTlsph::AssembleStress() {
// compute a characteristic time over which to average the plastic strain
double tav = 1000 * radius[i] / (Lookup[SIGNAL_VELOCITY][itype]);
- eff_plastic_strain_rate[i] -= eff_plastic_strain_rate[i] / tav;
- eff_plastic_strain_rate[i] += (plastic_strain_increment / dt) / tav;
- eff_plastic_strain_rate[i] = MAX(0.0, eff_plastic_strain_rate[i]);
+ eff_plastic_strain_rate[i] -= eff_plastic_strain_rate[i] * dt / tav;
+ eff_plastic_strain_rate[i] += plastic_strain_increment / tav;
+ eff_plastic_strain_rate[i] = MAX(0.0, eff_plastic_strain_rate[i]);
/*
* assemble total stress from pressure and deviatoric stress
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index dd639c34dbc3e4442a16c60875d01587f085ff1d..36494b0d493809c4ae10e9314bc58765a19ee674 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -734,7 +734,7 @@ void FixNHUef::end_of_step()
comm->borders();
domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
}
@@ -754,7 +754,7 @@ void FixNHUef::post_run()
comm->borders();
domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 9d257d99de871f599afe709a399d83b08bfdda18..4b1be77a061464728e8769f8fef48ef37d667c00 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -57,7 +57,7 @@ void Atom::map_init(int check)
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
- map_hash[map_nhash-1].next = -1;
+ if (map_nhash > 0) map_hash[map_nhash-1].next = -1;
}
// recreating: delete old map and create new one for array or hash
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index dcfd2ff131c1526b79175b15c92482e9cf1c8b29..aa1210caadf1f7247006daecdc7763a095a8b25f 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -712,13 +712,14 @@ void ComputeChunkAtom::compute_ichunk()
return;
}
- invoked_ichunk = update->ntimestep;
-
// assign chunk IDs to atoms
// will exclude atoms not in group or in optional region
// already invoked if this is same timestep as last setup_chunks()
+ // however, when between runs or using rerun, we need it again.
- if (update->ntimestep > invoked_setup) assign_chunk_ids();
+ if ((update->ntimestep > invoked_setup) || (invoked_ichunk < 0)) assign_chunk_ids();
+
+ invoked_ichunk = update->ntimestep;
// compress chunk IDs via hash of the original uncompressed IDs
// also apply discard rule except for binning styles which already did
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 4752002ac9319d4096fbeb5f1a3f1c4ae5d6ef83..48f12406b6ea06cb4fda7a20ed90fd4b85ef8bf0 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -209,7 +209,7 @@ void CreateBonds::many()
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
- neighbor->build();
+ neighbor->build(1);
// build neighbor list this command needs based on earlier request
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 489c5bf5d5f4ce5837d42ee64d8fcd04be3103f3..a5b15f5f52a848894b35467639f772779c9d831e 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -311,7 +311,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
- neighbor->build();
+ neighbor->build(1);
// build neighbor list this command needs based on earlier request
diff --git a/src/fix.cpp b/src/fix.cpp
index 80fa00f4b3a84c8f951ab85874d8ebe7d7d12808..297d184967617100ae2ea25804ec5beb9d7e1217 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -350,7 +350,6 @@ void Fix::v_tally(int n, int *list, double total, double *v)
void Fix::v_tally(int i, double *v)
{
-
if (vflag_global) {
virial[0] += v[0];
virial[1] += v[1];
@@ -384,7 +383,6 @@ void Fix::v_tally(int i, double *v)
void Fix::v_tally(int n, int i, double vn)
{
-
if (vflag_global)
virial[n] += vn;
diff --git a/src/group.cpp b/src/group.cpp
index 76275f301d34272e6e6d1c8572c37840eb6c73f6..93c9c12bcf8df5618cae05075181ba396787ae18 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -188,6 +188,12 @@ void Group::assign(int narg, char **arg)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
mask[i] |= bit;
+ // create an empty group
+
+ } else if (strcmp(arg[1],"empty") == 0) {
+
+ ; // nothing to do here
+
// style = type, molecule, id
// add to group if atom matches type/molecule/id or condition
diff --git a/src/integrate.h b/src/integrate.h
index 4ca3a788fa3d8f1754674a030cb0ce6d8b5d7c32..9a50fad1f74c3c5a20df76d7764bda389a57f537 100644
--- a/src/integrate.h
+++ b/src/integrate.h
@@ -23,7 +23,7 @@ class Integrate : protected Pointers {
Integrate(class LAMMPS *, int, char **);
virtual ~Integrate();
virtual void init();
- virtual void setup(int flag=1) = 0;
+ virtual void setup(int flag) = 0;
virtual void setup_minimal(int) = 0;
virtual void run(int) = 0;
virtual void cleanup() {}
diff --git a/src/kspace.cpp b/src/kspace.cpp
index c2113cdf767c899d733ed9dc3d44162ff140563f..07e117e162989adb3d894d1e3390a7e96757d727 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -315,10 +315,10 @@ double KSpace::estimate_table_accuracy(double q2_over_sqrt, double spr)
if (comm->me == 0) {
char str[128];
if (nctb)
- sprintf(str,"Using %d-bit tables for long-range coulomb",nctb);
+ sprintf(str," using %d-bit tables for long-range coulomb",nctb);
else
- sprintf(str,"Using polynomial approximation for long-range coulomb");
- error->warning(FLERR,str);
+ sprintf(str," using polynomial approximation for long-range coulomb");
+ error->message(FLERR,str);
}
if (nctb) {
diff --git a/src/library.cpp b/src/library.cpp
index 8f87d6fab240944bd523b5891b3279d41e204646..0544aa5a4a3538143cc7b7a8ec436b25f66d3964 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -203,7 +203,10 @@ void lammps_file(void *ptr, char *str)
BEGIN_CAPTURE
{
- lmp->input->file(str);
+ if (lmp->update->whichflag != 0)
+ lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run");
+ else
+ lmp->input->file(str);
}
END_CAPTURE
}
@@ -221,7 +224,10 @@ char *lammps_command(void *ptr, char *str)
BEGIN_CAPTURE
{
- result = lmp->input->one(str);
+ if (lmp->update->whichflag != 0)
+ lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run");
+ else
+ result = lmp->input->one(str);
}
END_CAPTURE
@@ -270,6 +276,13 @@ void lammps_commands_string(void *ptr, char *str)
{
LAMMPS *lmp = (LAMMPS *) ptr;
+ BEGIN_CAPTURE
+ {
+ if (lmp->update->whichflag != 0)
+ lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run");
+ }
+ END_CAPTURE
+
// make copy of str so can strtok() it
int n = strlen(str) + 1;
diff --git a/src/min.cpp b/src/min.cpp
index 653cac71e6af5b3a52a00d808a47319242593def..0caa9a9acf0584eac39ad0a55c8ddf634f56906e 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -245,7 +245,7 @@ void Min::setup(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
@@ -345,7 +345,7 @@ void Min::setup_minimal(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
}
@@ -508,7 +508,7 @@ double Min::energy_force(int resetflag)
modify->min_pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
if (modify->n_min_post_neighbor) {
modify->min_post_neighbor();
diff --git a/src/molecule.cpp b/src/molecule.cpp
index b93cf24e7efaa74bb0d84fc00c730dbba63c7e59..78dc4b82b3ed2374dbae7cafa4f3e5d296408c1e 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -144,17 +144,17 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (me == 0) {
if (screen)
fprintf(screen,"Read molecule %s:\n"
- " %d atoms with %d types\n %d bonds with %d types\n"
- " %d angles with %d types\n %d dihedrals with %d types\n"
- " %d impropers with %d types\n",
+ " %d atoms with max type %d\n %d bonds with max type %d\n"
+ " %d angles with max type %d\n %d dihedrals with max type %d\n"
+ " %d impropers with max type %d\n",
id,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
if (logfile)
fprintf(logfile,"Read molecule %s:\n"
- " %d atoms with %d types\n %d bonds with %d types\n"
- " %d angles with %d types\n %d dihedrals with %d types\n"
- " %d impropers with %d types\n",
+ " %d atoms with max type %d\n %d bonds with max type %d\n"
+ " %d angles with max type %d\n %d dihedrals with max type %d\n"
+ " %d impropers with max type %d\n",
id,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
diff --git a/src/neighbor.h b/src/neighbor.h
index 9244bc575d9b355780996e98e6fb4b63f9aa0651..c054cddb2b59d04dbfd723d8c405e66ea8cf2ad5 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -111,7 +111,7 @@ class Neighbor : protected Pointers {
int decide(); // decide whether to build or not
virtual int check_distance(); // check max distance moved since last build
void setup_bins(); // setup bins based on box and cutoff
- virtual void build(int topoflag=1); // build all perpetual neighbor lists
+ virtual void build(int); // build all perpetual neighbor lists
virtual void build_topology(); // pairwise topology neighbor lists
void build_one(class NeighList *list, int preflag=0);
// create a one-time pairwise neigh list
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
index cf608b5d595ab5d27cbc287b64b78a77efdb317a..d575f3eb1f572ceccb4bdbb59a624db44130da22 100644
--- a/src/npair_half_size_bin_newtoff.cpp
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -36,14 +36,13 @@ NPairHalfSizeBinNewtoff::NPairHalfSizeBinNewtoff(LAMMPS *lmp) : NPair(lmp) {}
void NPairHalfSizeBinNewtoff::build(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
index 662bf91d6e9606d4c00a1a42ce130c34beea17a6..da29cb2029aecc4e0db37e3d4aa1ee44a3f77c6d 100644
--- a/src/npair_half_size_bin_newton.cpp
+++ b/src/npair_half_size_bin_newton.cpp
@@ -35,14 +35,13 @@ NPairHalfSizeBinNewton::NPairHalfSizeBinNewton(LAMMPS *lmp) : NPair(lmp) {}
void NPairHalfSizeBinNewton::build(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp
index e70c0722804dad9ef06858a7d2f37d77aa33dd62..044847ba8ce9d38d534e5aecfc13e841e5d81a9b 100644
--- a/src/npair_half_size_bin_newton_tri.cpp
+++ b/src/npair_half_size_bin_newton_tri.cpp
@@ -36,14 +36,13 @@ NPairHalfSizeBinNewtonTri::NPairHalfSizeBinNewtonTri(LAMMPS *lmp) :
void NPairHalfSizeBinNewtonTri::build(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp
index e6f5cba657f79ec1318e4a15b2050e34d0c480e5..50a32c87ba5d3ed2ab5883eb7e47167f626adbca 100644
--- a/src/npair_half_size_nsq_newtoff.cpp
+++ b/src/npair_half_size_nsq_newtoff.cpp
@@ -36,14 +36,13 @@ NPairHalfSizeNsqNewtoff::NPairHalfSizeNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
void NPairHalfSizeNsqNewtoff::build(NeighList *list)
{
- int i,j,m,n,nn,bitmask;
+ int i,j,n,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
- tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp
index 78811170cbd50450234a70b1f580ab2a91df43fc..343172fb986c0a316d705c186a892aeee10a002d 100644
--- a/src/npair_half_size_nsq_newton.cpp
+++ b/src/npair_half_size_nsq_newton.cpp
@@ -37,7 +37,7 @@ NPairHalfSizeNsqNewton::NPairHalfSizeNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
void NPairHalfSizeNsqNewton::build(NeighList *list)
{
- int i,j,m,n,nn,itag,jtag,bitmask;
+ int i,j,n,itag,jtag,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp
index 075387f5b043cc857ddf2a234ebfc6a4f6c5ec15..b75856dde409a3e060cf1831f6ecc8684c965977 100644
--- a/src/npair_skip_size.cpp
+++ b/src/npair_skip_size.cpp
@@ -33,14 +33,10 @@ NPairSkipSize::NPairSkipSize(LAMMPS *lmp) : NPair(lmp) {}
void NPairSkipSize::build(NeighList *list)
{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
- tagint jtag;
+ int i,j,ii,jj,n,itype,jnum,joriginal;
int *neighptr,*jlist;
- tagint *tag = atom->tag;
int *type = atom->type;
- int nlocal = atom->nlocal;
-
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp
index 92eae285d0a37d03b55b8bb09ef95d2e2f2e53d0..8d728a3c0ad73074bb06b4786462f854fd0cc4a2 100644
--- a/src/npair_skip_size_off2on.cpp
+++ b/src/npair_skip_size_off2on.cpp
@@ -34,7 +34,7 @@ NPairSkipSizeOff2on::NPairSkipSizeOff2on(LAMMPS *lmp) : NPair(lmp) {}
void NPairSkipSizeOff2on::build(NeighList *list)
{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
+ int i,j,ii,jj,n,itype,jnum,joriginal;
tagint itag,jtag;
int *neighptr,*jlist;
diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp
index f2fca7b1284389c925650d6678cc0d7d14d87fc4..a04fc7782c2bcfdecd88d6f8e2df6b438bfc08a8 100644
--- a/src/npair_skip_size_off2on_oneside.cpp
+++ b/src/npair_skip_size_off2on_oneside.cpp
@@ -37,11 +37,9 @@ NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
void NPairSkipSizeOff2onOneside::build(NeighList *list)
{
- int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
- tagint jtag;
+ int i,j,ii,jj,n,itype,jnum,joriginal,flip,tmp;
int *surf,*jlist;
- tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1527180eacfcbe92c99efa871bab7b4a12f9e2bc
--- /dev/null
+++ b/src/pair_lj_cut_coul_wolf.cpp
@@ -0,0 +1,447 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Vishal Boddu (FAU)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_lj_cut_coul_wolf.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+PairLJCutCoulWolf::PairLJCutCoulWolf(LAMMPS *lmp) : Pair(lmp)
+{
+ single_enable = 0;
+ writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLJCutCoulWolf::~PairLJCutCoulWolf()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut_lj);
+ memory->destroy(cut_ljsq);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(lj4);
+ memory->destroy(offset);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+ double rsq,r2inv,r6inv,forcelj,factor_lj,forcecoul,factor_coul;
+ double prefactor;
+ double r;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
+
+ evdwl = 0.0;
+ ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_lj = force->special_lj;
+ double *special_coul = force->special_coul;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+
+ // self and shifted Coulombic energy
+
+ e_self = v_sh = 0.0;
+ e_shift = erfc(alf*cut_coul)/cut_coul;
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS
+ * exp(-alf*alf*cut_coul*cut_coul)) / cut_coul;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ qisq = qtmp*qtmp;
+ e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
+ if (eflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ prefactor = qqrd2e*qtmp*q[j]/r;
+ erfcc = erfc(alf*r);
+ erfcd = exp(-alf*alf*r*r);
+ v_sh = (erfcc - e_shift*r) * prefactor;
+ dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
+ forcecoul = dvdrr*rsq*prefactor;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ memory->create(cut_lj,n+1,n+1,"pair:cut");
+ memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(lj4,n+1,n+1,"pair:lj4");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::settings(int narg, char **arg)
+{
+ if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
+
+ alf = force->numeric(FLERR,arg[0]);
+ cut_lj_global = force->numeric(FLERR,arg[1]);
+ if (narg == 2) cut_coul = cut_lj_global;
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::coeff(int narg, char **arg)
+{
+ if (narg < 4 || narg > 5)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+
+ double cut_lj_one = cut_lj_global;
+ if (narg == 5) cut_lj_one = force->numeric(FLERR,arg[4]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ cut_lj[i][j] = cut_lj_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::init_style()
+{
+ if (!atom->q_flag)
+ error->all(FLERR,"Pair style lj/cut/coul/wolf requires atom attribute q");
+
+ cut_coulsq = cut_coul * cut_coul;
+
+ // request regular or rRESPA neighbor list
+
+ int irequest;
+ irequest = neighbor->request(this,instance_me);
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLJCutCoulWolf::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
+ sigma[i][i],sigma[j][j]);
+ sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
+ cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
+ }
+
+ double cut = MAX(cut_lj[i][j],cut_coul);
+ cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
+
+ lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
+ lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
+ lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
+ lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
+
+ if (offset_flag && (cut_lj[i][j] > 0.0)) {
+ double ratio = sigma[i][j] / cut_lj[i][j];
+ offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
+ } else offset[i][j] = 0.0;
+
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ lj4[j][i] = lj4[i][j];
+ offset[j][i] = offset[i][j];
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double sig2 = sigma[i][j]*sigma[i][j];
+ double sig6 = sig2*sig2*sig2;
+ double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
+ double rc6 = rc3*rc3;
+ double rc9 = rc3*rc6;
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ }
+
+ return cut;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::write_restart_settings(FILE *fp)
+{
+ fwrite(&alf,sizeof(double),1,fp);
+ fwrite(&cut_lj_global,sizeof(double),1,fp);
+ fwrite(&cut_coul,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::read_restart_settings(FILE *fp)
+{
+ int me = comm->me;
+ if (me == 0) {
+ fread(&alf,sizeof(double),1,fp);
+ fread(&cut_lj_global,sizeof(double),1,fp);
+ fread(&cut_coul,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ }
+ MPI_Bcast(&alf,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulWolf::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
+}
diff --git a/src/pair_lj_cut_coul_wolf.h b/src/pair_lj_cut_coul_wolf.h
new file mode 100644
index 0000000000000000000000000000000000000000..aa4e08f9b79c8eae654a6cd13a5d77daada9c9a2
--- /dev/null
+++ b/src/pair_lj_cut_coul_wolf.h
@@ -0,0 +1,70 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/cut/coul/wolf,PairLJCutCoulWolf)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CUT_COUL_WOLF_H
+#define LMP_PAIR_LJ_CUT_COUL_WOLF_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairLJCutCoulWolf : public Pair {
+ public:
+ PairLJCutCoulWolf(class LAMMPS *);
+ virtual ~PairLJCutCoulWolf();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+
+ protected:
+ double cut_lj_global;
+ double **cut_lj,**cut_ljsq;
+ double **epsilon,**sigma;
+ double **lj1,**lj2,**lj3,**lj4,**offset;
+ double cut_coul,cut_coulsq,alf;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+*/
diff --git a/src/respa.cpp b/src/respa.cpp
index 23cd941834482d3f5047602c8fa98e426f901ba4..18630c06d6fe8c525716cebd9bf5d689406dfe86 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -441,7 +441,7 @@ void Respa::setup(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
@@ -517,7 +517,7 @@ void Respa::setup_minimal(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
}
@@ -668,7 +668,7 @@ void Respa::recurse(int ilevel)
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
if (modify->n_post_neighbor) {
modify->post_neighbor();
diff --git a/src/respa.h b/src/respa.h
index 0b08b12bd7088220ce63000c054b3278cba34fe2..f910f0c666179f5d75247d9c1023490c221d86f8 100644
--- a/src/respa.h
+++ b/src/respa.h
@@ -48,7 +48,7 @@ class Respa : public Integrate {
Respa(class LAMMPS *, int, char **);
virtual ~Respa();
virtual void init();
- virtual void setup(int flag=1);
+ virtual void setup(int);
virtual void setup_minimal(int);
virtual void run(int);
virtual void cleanup();
diff --git a/src/run.cpp b/src/run.cpp
index 331754534287e9561b38c91a27e2234f0f7fdc67..37af977e3450f2b2b07ff38c3c35199447ddcc44 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -175,7 +175,7 @@ void Run::command(int narg, char **arg)
if (preflag || update->first_update == 0) {
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
} else output->setup(0);
timer->init();
@@ -216,7 +216,7 @@ void Run::command(int narg, char **arg)
if (preflag || iter == 0) {
lmp->init();
- update->integrate->setup();
+ update->integrate->setup(1);
} else output->setup(0);
timer->init();
diff --git a/src/verlet.cpp b/src/verlet.cpp
index d74906556b35c32bde5da26114a31cf7c9441b13..019f3f2f05b3f539cd9619b441dd77f290c804dd 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -120,7 +120,7 @@ void Verlet::setup(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
@@ -182,7 +182,7 @@ void Verlet::setup_minimal(int flag)
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
- neighbor->build();
+ neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
}
@@ -284,7 +284,7 @@ void Verlet::run(int n)
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
- neighbor->build();
+ neighbor->build(1);
timer->stamp(Timer::NEIGH);
if (n_post_neighbor) {
modify->post_neighbor();
diff --git a/src/verlet.h b/src/verlet.h
index 29bd3f16b34424d16ea5abd0a0f48b7715ef6829..e71932a8615e9d1eefa5a2e560a9faccf8681351 100644
--- a/src/verlet.h
+++ b/src/verlet.h
@@ -29,7 +29,7 @@ class Verlet : public Integrate {
Verlet(class LAMMPS *, int, char **);
virtual ~Verlet() {}
virtual void init();
- virtual void setup(int flag=1);
+ virtual void setup(int flag);
virtual void setup_minimal(int);
virtual void run(int);
void cleanup();
diff --git a/src/version.h b/src/version.h
index f544f0203ca371c37d6f543fb5156a36e0c38241..8342aa8ef11c107fac6e5e2d205739e9e2f7aa19 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "17 Jan 2018"
+#define LAMMPS_VERSION "22 Feb 2018"
diff --git a/tools/msi2lmp/src/ReadCarFile.c b/tools/msi2lmp/src/ReadCarFile.c
index 73209bc99454a4a83f5ae83cdfb25d5ad5f729c1..c6db96cf922658eb33c0c5b6766e76e57219cb5e 100644
--- a/tools/msi2lmp/src/ReadCarFile.c
+++ b/tools/msi2lmp/src/ReadCarFile.c
@@ -73,7 +73,6 @@ void ReadCarFile(void)
int skip; /* lines to skip at beginning of file */
double lowest, highest; /* temp coordinate finding variables */
double total_q;
- double sq_c;
double cos_alpha; /* Added by SLTM Sept 13, 2010 */
double cos_gamma;
double sin_gamma;
@@ -261,7 +260,7 @@ void ReadCarFile(void)
box[2][k] = 0.0;
}
} else {
- sq_c = pbc[2]*pbc[2];
+ double ly,lz;
cos_alpha = cos(pbc[3]*PI_180);
cos_gamma = cos(pbc[5]*PI_180);
sin_gamma = sin(pbc[5]*PI_180);
@@ -275,16 +274,23 @@ void ReadCarFile(void)
B = pbc[1];
C = pbc[2];
+ /* compute xy, xz, and yz */
+ box[2][0] = B * cos_gamma;
+ box[2][1] = C * cos_beta;
+ if (fabs(sin_gamma) > 0.0001)
+ box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma;
+ else box[2][2] = 0.0;
box[0][0] = -0.5*A + center[0] + shift[0];
box[1][0] = 0.5*A + center[0] + shift[0];
- box[0][1] = -0.5*B*sin_gamma + center[1] + shift[1];
- box[1][1] = 0.5*B*sin_gamma + center[1] + shift[1];
- box[0][2] = -0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
- box[1][2] = 0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
- box[2][0] = B * cos_gamma; /* This is xy SLTM */
- box[2][1] = C * cos_beta; /* This is xz SLTM */
- box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; /* This is yz SLTM */
+
+ /* compute adjusted box length for y and z and apply */
+ ly = sqrt(B*B - box[2][0]*box[2][0]);
+ lz = sqrt(C*C - box[2][1]*box[2][1] - box[2][2]*box[2][2]);
+ box[0][1] = -0.5*ly + center[1] + shift[1];
+ box[1][1] = 0.5*ly + center[1] + shift[1];
+ box[0][2] = -0.5*lz + center[2] + shift[2];
+ box[1][2] = 0.5*lz + center[2] + shift[2];
}
}
diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c
index 15cfddd258587b67e4ff01093fc50188589ea820..b0bc7815baf5d4786d28ef1d8524a7313034c2ed 100644
--- a/tools/msi2lmp/src/msi2lmp.c
+++ b/tools/msi2lmp/src/msi2lmp.c
@@ -273,7 +273,7 @@ int main (int argc, char *argv[])
shift[2] = atof(argv[++n]);
} else if (strncmp(argv[n],"-i",2) == 0 ) {
iflag = 1;
- } else if (strncmp(argv[n],"-n",4) == 0 ) {
+ } else if (strncmp(argv[n],"-n",2) == 0 ) {
centerflag = 0;
} else if (strncmp(argv[n],"-o",2) == 0 ) {
hintflag = 0;
diff --git a/tools/pymol_asphere/src/error.cpp b/tools/pymol_asphere/src/error.cpp
index 0bbd0905669b8d6724abda9d1610f32822017994..9491ca04a4c23763b143e2833030df03694fe466 100644
--- a/tools/pymol_asphere/src/error.cpp
+++ b/tools/pymol_asphere/src/error.cpp
@@ -13,7 +13,8 @@
#include "error.h"
#include <cstring>
-
+#include <cstdlib>
+
Notice::Notice() {
nullout=new ostream(NULL);
noteout=&cout;