diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html
index 9eeebfac7db194adfb0af3cac3a477b4522cf8ad..a535b871a97db615d91451c9162ed38a9fdf905c 100644
--- a/doc/src/USER/atc/man_add_molecule.html
+++ b/doc/src/USER/atc/man_add_molecule.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -23,21 +37,21 @@ 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 06b8c0b91cd4638f530f9997da17384d6ff93492..5166ccfa2d3a0d5ea1367cd077a297f459cba2a7 100644
--- a/doc/src/USER/atc/man_add_species.html
+++ b/doc/src/USER/atc/man_add_species.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -23,21 +37,21 @@ 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 351447e07ead1bd958c6edc470b7b9279e21669c..47ea0f20c97ef6d18ffd1f184fa5a06e6b2dac46 100644
--- a/doc/src/USER/atc/man_atom_element_map.html
+++ b/doc/src/USER/atc/man_atom_element_map.html
@@ -7,30 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 def587b98b90ede0f1742972e6d167c1c6bdfe80..9161b54f32fd1af5d9f6a15ef1d3682c8fd5865b 100644
--- a/doc/src/USER/atc/man_atom_weight.html
+++ b/doc/src/USER/atc/man_atom_weight.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -24,22 +38,22 @@ 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 e0988cb98e71d1fc36db9598ab5f4c450eefcd94..3507a5598b0259053fcfa4ef5d083201ede27b8d 100644
--- a/doc/src/USER/atc/man_atomic_charge.html
+++ b/doc/src/USER/atc/man_atomic_charge.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 ad7fe96cf4c6edc4c28f66c985d8d6a18dd87194..6694311981d58cd6fe796b90104b4db195fdbb67 100644
--- a/doc/src/USER/atc/man_boundary.html
+++ b/doc/src/USER/atc/man_boundary.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 a68d1a252f04a86e0888efcb63395df075f6f2f4..3a7cb141a76731da680bc2508414b205f43b6d3b 100644
--- a/doc/src/USER/atc/man_boundary_dynamics.html
+++ b/doc/src/USER/atc/man_boundary_dynamics.html
@@ -7,24 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 0e13df41e3337d417bac08c06751d2f0aac0b08d..2e2fce7bdbe5aab8d7d3b5753a4747d603ff7e75 100644
--- a/doc/src/USER/atc/man_boundary_faceset.html
+++ b/doc/src/USER/atc/man_boundary_faceset.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 6ba17562eeb2854136bcdc84d9d0a989cb43aaf9..e1933a9465af444ea83053b7b35074f8c1cae343 100644
--- a/doc/src/USER/atc/man_boundary_integral.html
+++ b/doc/src/USER/atc/man_boundary_integral.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<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>
-<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_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index 16abc2593f8979dafb7c969da99b445e13381107..a74acda5e95b99f16f27d60310076f0147570113 100644
--- a/doc/src/USER/atc/man_consistent_fe_initialization.html
+++ b/doc/src/USER/atc/man_consistent_fe_initialization.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 da43a1d8630a6241de3deb984b40f4fd01eee975..304b4bec66e94d6bf7eef91d42897d92d417c94e 100644
--- a/doc/src/USER/atc/man_contour_integral.html
+++ b/doc/src/USER/atc/man_contour_integral.html
@@ -7,32 +7,46 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<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>
-<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.html b/doc/src/USER/atc/man_control.html
index b63c07b32798484501d4de4e13cdbb1d14407992..2c42fa2d6aa6c93c10f478b65b43c324e159804d 100644
--- a/doc/src/USER/atc/man_control.html
+++ b/doc/src/USER/atc/man_control.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -34,22 +48,22 @@ 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 03e12641642d709d94c78b5c064d04594da381c9..fd9aadf1d7ba45df6926aff2c888f53c293b372a 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -32,21 +46,21 @@ 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 0f70c595cce8b12260e8e5ab03e7eb8d7dbfe255..b6af089baf9bfe5680582b1ef138c044da13aea9 100644
--- a/doc/src/USER/atc/man_control_thermal.html
+++ b/doc/src/USER/atc/man_control_thermal.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -34,25 +48,25 @@ 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 45f4d9246ecb15ed223c67158df61179c44c75e6..2a939d16932749e4b44958d9afdcdd68957140e3 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
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 b57a276e31a040522f4718451e61db50a4ed80fa..fd8986b19d5f805bfd1d1a6ebc084c46e3001bbb 100644
--- a/doc/src/USER/atc/man_decomposition.html
+++ b/doc/src/USER/atc/man_decomposition.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -20,20 +34,20 @@ 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 bb9a4f72bd8cae325f3a10e6890d2b1357c8201e..ab00b5d45f784a534f16663ba310386d9ffca0fb 100644
--- a/doc/src/USER/atc/man_electron_integration.html
+++ b/doc/src/USER/atc/man_electron_integration.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,20 +34,20 @@ 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>
+<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 08106f1174d20fcbcc4472e3a5b8942c8b192e69..ba19dbf53a3cbccc089bd50ad5ea3fcab67d3525 100644
--- a/doc/src/USER/atc/man_equilibrium_start.html
+++ b/doc/src/USER/atc/man_equilibrium_start.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 dca429e3b8ff2bb358a2197b4447848777e30443..5b3b4315e1fe2aea26f3570f9396ba4a10b5e632 100644
--- a/doc/src/USER/atc/man_extrinsic_exchange.html
+++ b/doc/src/USER/atc/man_extrinsic_exchange.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<h4><a class="anchor" id="related">
+related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</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_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html
index d83821b867efc38cd8826a42194a755766f29d7e..aa1b6f6bb320980f4da00a59bd1ec4a8f2b71ebe 100644
--- a/doc/src/USER/atc/man_fe_md_boundary.html
+++ b/doc/src/USER/atc/man_fe_md_boundary.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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..3b6f0ddc34f07b8d37aaf1044a89b4c2d134fdc7 100644
--- a/doc/src/USER/atc/man_fem_mesh.html
+++ b/doc/src/USER/atc/man_fem_mesh.html
@@ -3,21 +3,34 @@
<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>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
+<h3><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" name="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>
+<h4><a class="anchor" name="examples">
+examples</a></h4>
+<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h4><a class="anchor" name="description">
+description</a></h4>
+Creates a uniform mesh in a rectangular region <h4><a class="anchor" name="restrictions">
+restrictions</a></h4>
+creates only uniform rectangular grids in a rectangular region <h4><a class="anchor" name="related">
+related</a></h4>
+<h4><a class="anchor" name="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>
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index bca799804f93ef5ef4bf7b327c05287dd3ea0cac..68eb5ef370de686ecde4623eb2d5084e25b151fc 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -7,33 +7,47 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 8b7d7ad58ec44a9b6c1423633042f6b55682a908..919dff505f3cbc5708fcc047d902b0a92fd42d38 100644
--- a/doc/src/USER/atc/man_filter_type.html
+++ b/doc/src/USER/atc/man_filter_type.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 0e14498ffefe73b8125da5bd2cd9e9fd3502fbff..9e82ded3de5d14f68ac6d198a760b5e330a74aaf 100644
--- a/doc/src/USER/atc/man_fix_atc.html
+++ b/doc/src/USER/atc/man_fix_atc.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -26,15 +40,15 @@ 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>
@@ -122,16 +136,16 @@ 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>
@@ -231,8 +245,8 @@ 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 46400e9103d5e0333e621dcb5e0ccb37c05b184d..a5b98d8c642d6236c31eaf18e9eed6f3501a6884 100644
--- a/doc/src/USER/atc/man_fix_flux.html
+++ b/doc/src/USER/atc/man_fix_flux.html
@@ -7,32 +7,46 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 4745e241c672bf2941ac1b2d0a67ac05446bb398..b8d20002b5ec7a661fb5af4d6b31c5f624ac82d1 100644
--- a/doc/src/USER/atc/man_fix_nodes.html
+++ b/doc/src/USER/atc/man_fix_nodes.html
@@ -7,34 +7,48 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 e6fb1430a6cdf95d291476b51ecc3816b81e3df0..9c4ea9340deffc19fd53ece1ab0778ee94e67622 100644
--- a/doc/src/USER/atc/man_hardy_computes.html
+++ b/doc/src/USER/atc/man_hardy_computes.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -23,8 +37,8 @@ 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/>
@@ -32,20 +46,20 @@ 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>
+<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 c393bcba2aba169bd3a2226fee0ffe5385b16417..79cbbb5d5653fa2073b6f5188b130ecc1e58a3ea 100644
--- a/doc/src/USER/atc/man_hardy_fields.html
+++ b/doc/src/USER/atc/man_hardy_fields.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -44,24 +58,24 @@ 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>
+<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>
-<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_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 12a80c21660d6a77679b8a6aaddedb53af799d3e..30016b591afc02fa8ee38aee08d9442895dc1550 100644
--- a/doc/src/USER/atc/man_hardy_gradients.html
+++ b/doc/src/USER/atc/man_hardy_gradients.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -21,21 +35,21 @@ 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>
+<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>
-<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>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 6c8ddd99234930aa392e92d2987ec2f3a50ac12c..a37fdd22d959d638628b6f256bac50e1e0a97af0 100644
--- a/doc/src/USER/atc/man_hardy_kernel.html
+++ b/doc/src/USER/atc/man_hardy_kernel.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -28,22 +42,22 @@ 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="../../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="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 bc2d71a17b964ca35500656b0272295d901f517c..043926d555f854656253c57b46293e82dc16f3ac 100644
--- a/doc/src/USER/atc/man_hardy_on_the_fly.html
+++ b/doc/src/USER/atc/man_hardy_on_the_fly.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,24 +34,24 @@ 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>
+<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>
-<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>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 4edec12d688a55ec961b248b57fa8f25797f69a1..775df82f94673a39b1f1d5e455ef8bcca800193c 100644
--- a/doc/src/USER/atc/man_hardy_rates.html
+++ b/doc/src/USER/atc/man_hardy_rates.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -21,22 +35,22 @@ 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>
+<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>
-<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>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 539d8afd59ca3c888fae333b14c352702f85232e..429bd25af6ebfb024f6f5f7bd555b3a6dca5b46f 100644
--- a/doc/src/USER/atc/man_initial.html
+++ b/doc/src/USER/atc/man_initial.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 5a8704c46f6feb152516daef08fddda55c24c6d8..2f2987ec6872ddfea270dd27df7878c3d4f57f7a 100644
--- a/doc/src/USER/atc/man_internal_atom_integrate.html
+++ b/doc/src/USER/atc/man_internal_atom_integrate.html
@@ -7,18 +7,32 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 bf1cb007f68be9150aae581308d6be4d52138fde..dbd1d1e026ecd8a641e59ba48eb654ba106ace6e 100644
--- a/doc/src/USER/atc/man_internal_element_set.html
+++ b/doc/src/USER/atc/man_internal_element_set.html
@@ -7,30 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 8ad3399e8634b43e595c29d02847dab41cb821a7..1a36ab460658d68312ad8b29015e28931e3c1900 100644
--- a/doc/src/USER/atc/man_internal_quadrature.html
+++ b/doc/src/USER/atc/man_internal_quadrature.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 e2702cd9fc96cb4315b29b7178f53e52c602b164..f87735b38beb5286a636d0e2e742e961963f5867 100644
--- a/doc/src/USER/atc/man_kernel_function.html
+++ b/doc/src/USER/atc/man_kernel_function.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -28,21 +42,21 @@ 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="../../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="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 e4355042335929bfa5961e44c1211a98cb6ee947..8b729f567b1177a51b74141aa9e9252b61fa19a0 100644
--- a/doc/src/USER/atc/man_localized_lambda.html
+++ b/doc/src/USER/atc/man_localized_lambda.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 43eee362e2237d51b5fe8f9c69692b518b5de0c2..a38edfff09f3285adad74e1f81bebc66a7b2df2e 100644
--- a/doc/src/USER/atc/man_lumped_lambda_solve.html
+++ b/doc/src/USER/atc/man_lumped_lambda_solve.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 07cf7a9418c0e9c37400225b4ab87baf13ff6ec5..951b5c1911c559eb1df9753192f1647afc2076d6 100644
--- a/doc/src/USER/atc/man_mask_direction.html
+++ b/doc/src/USER/atc/man_mask_direction.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 40f489985d192cac7c6ebaab2742bca04796250d..4661348e5517b24be9646681ecffaf59548460d0 100644
--- a/doc/src/USER/atc/man_mass_matrix.html
+++ b/doc/src/USER/atc/man_mass_matrix.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 8460b04a827da0254641d6f130ed5eeb17fa4607..956642bd9d5f888c6978ebf13609fb13f72e1823 100644
--- a/doc/src/USER/atc/man_material.html
+++ b/doc/src/USER/atc/man_material.html
@@ -7,27 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 5318e60cd1ed8040dd6e0615775efc6598b16d9c..7b5ea6bd60ce8fb17f912fb3f086c3eee8bd08e3 100644
--- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html
+++ b/doc/src/USER/atc/man_mesh_add_to_nodeset.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 c128d0391669390a9f62e6f83f5756e6d2c8e00f..d4ea2be031a813571e6e33f3742371bae6dad52a 100644
--- a/doc/src/USER/atc/man_mesh_create.html
+++ b/doc/src/USER/atc/man_mesh_create.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,21 +34,21 @@ 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 9d87a5be37027676113250cd3fa19873a6a9af65..188d85ceff5d522a06c05c8104ef48272cefba6e 100644
--- a/doc/src/USER/atc/man_mesh_create_elementset.html
+++ b/doc/src/USER/atc/man_mesh_create_elementset.html
@@ -7,30 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 ddbeb7eccfc5ea3e0ea2ef0e26308673170fd258..a406cace8b89e85adca53d31053d5914b9ec22e0 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_box.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_box.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,19 +34,19 @@ 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 af79885ed5c83b40eb468cbba5e4c9c35c330389..4f21be0def7eeb6f208a2137b0cc4aa9440ae8ea 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_plane.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,19 +34,19 @@ 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 32ac7f67e176a5bb1c3fd623f39106505674f75f..4c4fb68fe721f65be5e8f635f8705385ca502686 100644
--- a/doc/src/USER/atc/man_mesh_create_nodeset.html
+++ b/doc/src/USER/atc/man_mesh_create_nodeset.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 d43fe915653c8cbb4a4a4c07d728bd64b7d35602..071b67c1e105baf3dafad737dca62439298e3724 100644
--- a/doc/src/USER/atc/man_mesh_delete_elements.html
+++ b/doc/src/USER/atc/man_mesh_delete_elements.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 0fba4885ae3a3b18f679904391162511a21d417d..5e45d8dfa2b4232783cc6e61b9b4412015d6e7d5 100644
--- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
+++ b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 fb1d91f1530cd32950ccfc33ec02729f091037b2..95a0c10ed4f23d976fc91666b05fcf2c9e853556 100644
--- a/doc/src/USER/atc/man_mesh_output.html
+++ b/doc/src/USER/atc/man_mesh_output.html
@@ -7,27 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 f5d5e4873da9b122c65bc0698dc7e09c5711406c..dc1e987d877a50ff739a46588947e78b02e99d83 100644
--- a/doc/src/USER/atc/man_mesh_quadrature.html
+++ b/doc/src/USER/atc/man_mesh_quadrature.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 10bf2a644ab9668d27db43919f53e2b2005dac6d..e108177b9c25a74bd9722a3befc265b220cee080 100644
--- a/doc/src/USER/atc/man_mesh_read.html
+++ b/doc/src/USER/atc/man_mesh_read.html
@@ -7,30 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 e484b0466dbd650b1d5f109b6d736ad085ad3053..05208a3488aa24fb662d3f14336d3d731edf665e 100644
--- a/doc/src/USER/atc/man_mesh_write.html
+++ b/doc/src/USER/atc/man_mesh_write.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 e4ad7256b9e757b078fcb5c86d3049774e2de12b..9721d4dadc0f3ad12f482d87efb31400b702563a 100644
--- a/doc/src/USER/atc/man_momentum_time_integration.html
+++ b/doc/src/USER/atc/man_momentum_time_integration.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -21,24 +35,24 @@ 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>
+<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>
-<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_output.html b/doc/src/USER/atc/man_output.html
index 892424a902cfb7dc886e73966b1a0b969b467573..99196ded15127b0b2992e0e5487f43a47aa0e7ee 100644
--- a/doc/src/USER/atc/man_output.html
+++ b/doc/src/USER/atc/man_output.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -25,23 +39,23 @@ 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>
+<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>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<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 ae1da8d878fad4b74b43c0176053f9f5d9e9477e..03780e58e051e6d22a5f5831e80c5ce5d2fe32d2 100644
--- a/doc/src/USER/atc/man_output_elementset.html
+++ b/doc/src/USER/atc/man_output_elementset.html
@@ -7,32 +7,46 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<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>
-<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_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html
index 3005057d0d85062d7191d2f0ef61d70128e6d183..90536b4cb98d3c8b98657f603aff67f6c215fff4 100644
--- a/doc/src/USER/atc/man_output_nodeset.html
+++ b/doc/src/USER/atc/man_output_nodeset.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,20 +34,20 @@ 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>
+<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>
-<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_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html
index 0393b29d56f35f7c8f614ea7898e7e0dc4af6b2c..3c6d65432c297778ab3eb6896c477718f483e219 100644
--- a/doc/src/USER/atc/man_pair_interactions.html
+++ b/doc/src/USER/atc/man_pair_interactions.html
@@ -7,28 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 52022222f1efaf4fa3278b9902fe14b310832d81..2aa4be52a5e43af3bfda9e5f055c2396a4063070 100644
--- a/doc/src/USER/atc/man_poisson_solver.html
+++ b/doc/src/USER/atc/man_poisson_solver.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 b6da026bc83688f669515bb8ebec00088b4341ed..1e7c0be0e81c9088c8fb8b2367a27db7a5c7fbf4 100644
--- a/doc/src/USER/atc/man_read_restart.html
+++ b/doc/src/USER/atc/man_read_restart.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 0e288c9bee20864ff1883368fbb752d8c6b5576f..0a850dcac3b601289ee6fd05cfed048d9a332d86 100644
--- a/doc/src/USER/atc/man_remove_molecule.html
+++ b/doc/src/USER/atc/man_remove_molecule.html
@@ -7,32 +7,46 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 837a2a94e462a16ba2bf71d8a18b7ca2fe401831..f550e2d024d5b2027a457c80e65ab0bc09b6a922 100644
--- a/doc/src/USER/atc/man_remove_source.html
+++ b/doc/src/USER/atc/man_remove_source.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 0fc06d1cf9563a5846f0ee98b77bdb933e664260..ad563fcd79a85e5c9e0faaf1fb86542db1538bb0 100644
--- a/doc/src/USER/atc/man_remove_species.html
+++ b/doc/src/USER/atc/man_remove_species.html
@@ -7,32 +7,46 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 bc9ca16806f4f14509a0c4b24291069937b74a4f..4262ce7b4a738d35af432478752e2aabe65b8767 100644
--- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html
+++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
@@ -7,27 +7,41 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 a20cf9d0bf059a57f317e986fb1c4133114811f5..28a95599003c9eaf28a6016c6000d2f88391976f 100644
--- a/doc/src/USER/atc/man_reset_time.html
+++ b/doc/src/USER/atc/man_reset_time.html
@@ -7,43 +7,57 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 ba2544edc4171ef1a522cd99cb995b601539fd01..988a2cac509a0b4165ed8c074751f5c89233a57e 100644
--- a/doc/src/USER/atc/man_sample_frequency.html
+++ b/doc/src/USER/atc/man_sample_frequency.html
@@ -7,30 +7,44 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<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>
-<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> 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 993d9948d8fd157e3001f0699e98ed3016298654..6543a6458ac562fada49eda8de1e01da6a16f4de 100644
--- a/doc/src/USER/atc/man_set.html
+++ b/doc/src/USER/atc/man_set.html
@@ -7,34 +7,48 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
+<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>
-<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>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 81cb7cee4a56e0192f37311a28da946c8eaa50ed..5b8f47f483da997cca9369e50c5a096aea7720a1 100644
--- a/doc/src/USER/atc/man_source.html
+++ b/doc/src/USER/atc/man_source.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 80b66edb80f119be669823f314df8aed2c9f50d3..3ce3342458ead42b1865e942f1965641d51d2102 100644
--- a/doc/src/USER/atc/man_source_integration.html
+++ b/doc/src/USER/atc/man_source_integration.html
@@ -7,24 +7,38 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 18f89798ccbdf00c45bedde32e8a63df9648fcab..f7d212cad218af70eee77c3c6aca249686854589 100644
--- a/doc/src/USER/atc/man_temperature_definition.html
+++ b/doc/src/USER/atc/man_temperature_definition.html
@@ -7,25 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 8cceba845dc2afe8496eda2279f0abf0774b27e1..c9205550e9ff77d548f439fc2e8d250880fc6386 100644
--- a/doc/src/USER/atc/man_thermal_time_integration.html
+++ b/doc/src/USER/atc/man_thermal_time_integration.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -21,23 +35,23 @@ 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>
+<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>
-<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_time_filter.html b/doc/src/USER/atc/man_time_filter.html
index d75dc0703f9dc7b7074c29798e56b0ff21e80aaa..02b8bcabaa4ab939c8613f8835e43b458834605b 100644
--- a/doc/src/USER/atc/man_time_filter.html
+++ b/doc/src/USER/atc/man_time_filter.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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>
@@ -20,22 +34,22 @@ 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 c9b13d4094d6a062acf5666b1e1194fa323dbbc9..d77cf879c4137ee99d6664cb8b59fb61aff3e667 100644
--- a/doc/src/USER/atc/man_track_displacement.html
+++ b/doc/src/USER/atc/man_track_displacement.html
@@ -7,26 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 786a3f243acf94c04bddb52356f15f4fcb206167..76d24653f11df14d8c5b6ec08f026cadea489905 100644
--- a/doc/src/USER/atc/man_unfix_flux.html
+++ b/doc/src/USER/atc/man_unfix_flux.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 08266b4012523dc5bfbbd4e8c3f0ae37d020ae18..4ef1460138714eb9868b0b70a9aa449bfe4fc7eb 100644
--- a/doc/src/USER/atc/man_unfix_nodes.html
+++ b/doc/src/USER/atc/man_unfix_nodes.html
@@ -7,31 +7,45 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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 c91a51487c3cd5b55e5fd9c0a0ccec376d4896dd..864b9e43f983bb6e4be3889554f35d8ff23a9585 100644
--- a/doc/src/USER/atc/man_write_atom_weights.html
+++ b/doc/src/USER/atc/man_write_atom_weights.html
@@ -7,12 +7,26 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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/>
@@ -20,19 +34,19 @@ 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 42f43e3e9caa7285c7df48ece158d7e02f1fe2cc..8c0dae9f6f705f924802eaef635c137bdba050f4 100644
--- a/doc/src/USER/atc/man_write_restart.html
+++ b/doc/src/USER/atc/man_write_restart.html
@@ -7,29 +7,43 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
+<div style="text-align: right; padding: 5px; margin-bottom: -1.6em; display: block;">
+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="../../Section_commands.html#comm">Commands</a>
+</div>
+<div style="text-align: center; padding: 5px; margin-bottom: -1.6em; display: block;">
+ USER-AtC Manual
+</div>
+<div style="text-align: left; padding: 5px; margin-bottom: 0px; display: inline;">
+ <a href="../../Manual.html">LAMMPS Manual</a> »
+ <a href="../../fix_atc.html">fix atc command</a>
+</div>
+
+<hr>
+
<!-- Generated by Doxygen 1.6.1 -->
<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