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<div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -42,7 +30,7 @@ description</a></h2> <p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/> +<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> diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html index 3723cf98bf36d1bca05d04c3735f6e9a3209a2fd..08106f1174d20fcbcc4472e3a5b8942c8b192e69 100644 --- a/doc/src/USER/atc/man_equilibrium_start.html +++ b/doc/src/USER/atc/man_equilibrium_start.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - 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<div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index cf5c93590a2f561755953ffc56108911d1e13e4c..4745e241c672bf2941ac1b2d0a67ac05446bb398 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - 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</ul> - </div> -</div> <div class="contents"> @@ -50,7 +38,7 @@ description</a></h2> </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/> +<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"> diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index 1f55fd5e3702cb8cbaa4f3f59e4ab7e2ebf3657f..c393bcba2aba169bd3a2226fee0ffe5385b16417 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -68,7 +56,7 @@ description</a></h2> will only output the velocity and temperature fields. </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p> +<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> <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> diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 708fecbca1dedd4470e5b6e6e15090b37aec4a48..12a80c21660d6a77679b8a6aaddedb53af799d3e 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -43,7 +31,7 @@ description</a></h2> <p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<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"> diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index 3d81b367dd0e59c39be54580b80069c147d84cf6..6c8ddd99234930aa392e92d2987ec2f3a50ac12c 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -51,7 +39,7 @@ restrictions</a></h2> <p>Must be used with the hardy AtC fix <br/> For bar kernel types, half-width oriented along x-direction <br/> For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/> - ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> + ( 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"> diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html index d140cf6840e290a81e312aab76129992cf5ca5ed..bc2d71a17b964ca35500656b0272295d901f517c 100644 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ b/doc/src/USER/atc/man_hardy_on_the_fly.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -45,7 +33,7 @@ description</a></h2> </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<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"> diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html index ab0315cb65b179cf01b60309711d2d9c2ba87942..4edec12d688a55ec961b248b57fa8f25797f69a1 100644 --- a/doc/src/USER/atc/man_hardy_rates.html +++ b/doc/src/USER/atc/man_hardy_rates.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -44,7 +32,7 @@ description</a></h2> </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<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"> diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index c0a0be38523ed357b7806b006574cd5a3f08e5c0..539d8afd59ca3c888fae333b14c352702f85232e 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - 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<div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> @@ -50,7 +38,7 @@ restrictions</a></h2> <p>Must be used with the hardy AtC fix <br/> For bar kernel types, half-width oriented along x-direction <br/> For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/> - ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> + ( 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"> diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index 5dadb9d7304aaa0b764905fccdae458483b170e9..e4355042335929bfa5961e44c1211a98cb6ee947 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - 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It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p> <h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<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"> diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html index 833b2a866f4d28ad552ea2c257022dd0a77baacc..81cb7cee4a56e0192f37311a28da946c8eaa50ed 100644 --- a/doc/src/USER/atc/man_source.html +++ b/doc/src/USER/atc/man_source.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - 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<li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - </ul> - </div> -</div> <div class="contents"> diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html index c2f636134f09d21311c85498570ff4b6078c56ac..8cceba845dc2afe8496eda2279f0abf0774b27e1 100644 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ b/doc/src/USER/atc/man_thermal_time_integration.html @@ -8,18 +8,6 @@ </head> <body> <!-- Generated by Doxygen 1.6.1 --> -<div class="navigation" id="top"> - <div class="tabs"> - <ul> - <li><a href="index.html"><span>Main Page</span></a></li> - <li class="current"><a href="pages.html"><span>Related Pages</span></a></li> - <li><a href="namespaces.html"><span>Namespaces</span></a></li> - <li><a href="annotated.html"><span>Classes</span></a></li> - <li><a href="files.html"><span>Files</span></a></li> - <li><a href="dirs.html"><span>Directories</span></a></li> - 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