diff --git a/doc/USER/atc/man_atom_element_map.html b/doc/USER/atc/man_atom_element_map.html index 33bd8e692a9ba6ea1ff811b718d28c9a2e822750..3073c0f9209f52a9cfe50db2f602ae0067c3ec98 100644 --- a/doc/USER/atc/man_atom_element_map.html +++ b/doc/USER/atc/man_atom_element_map.html @@ -1,26 +1,52 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer atom_element_map</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_atom_element_map">fix_modify AtC transfer atom_element_map</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC atom_element_map</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC transfer atom_element_map <eulerian|lagrangian> <frequency> <br> +<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" name="examples"> +<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> -<code> fix_modify atc transfer atom_element_map eulerian 100 </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -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. <h2><a class="anchor" name="restrictions"> +<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> -Cannot change map type after initialization. <h2><a class="anchor" name="related"> +<p>Cannot change map type after initialization. </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -lagrangian <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>lagrangian </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_boundary_integral.html b/doc/USER/atc/man_boundary_integral.html index 7f8379d9b08bf1cec6c29fe9b45abfd88f29e3be..3e78f12963f3c44e01c9ab71bcbff511fc02a3e8 100644 --- a/doc/USER/atc/man_boundary_integral.html +++ b/doc/USER/atc/man_boundary_integral.html @@ -1,26 +1,53 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC boundary_integral</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_boundary_integral">fix_modify AtC boundary_integral</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC output boundary_integral</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC transfer boundary_integral [field] faceset [name]<ul> -<li>field (string) : name of hardy field</li><li>name (string) : name of faceset </li></ul> -<h2><a class="anchor" name="examples"> +<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> -<code> fix_modify AtC transfer boundary_integral stress faceset loop1 </code> <br> - <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/> + </p> +<h2><a class="anchor" id="description"> description</a></h2> -Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_contour_integral.html b/doc/USER/atc/man_contour_integral.html index b87b2567bf07ff63b53930f5e2644eeb2b969b96..c321605e884f97b6c3e65c2381bab5c0bbe9ce2a 100644 --- a/doc/USER/atc/man_contour_integral.html +++ b/doc/USER/atc/man_contour_integral.html @@ -1,26 +1,54 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC contour_integral</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_contour_integral">fix_modify AtC contour_integral</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC output contour_integral</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC transfer contour_integral [field] faceset [name] <axis [x | y | z]><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" name="examples"> +<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> -<code> fix_modify AtC transfer contour_integral stress faceset loop1 </code> <br> - <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/> + </p> +<h2><a class="anchor" id="description"> description</a></h2> -Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_electron_integration.html b/doc/USER/atc/man_electron_integration.html index dbde3d777a64c9e9c60c48cf119f1730fea491eb..b14c14d86d5dfbf4ef71a635335f0717af98fa4a 100644 --- a/doc/USER/atc/man_electron_integration.html +++ b/doc/USER/atc/man_electron_integration.html @@ -1,30 +1,56 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix_modify AtC extrinsic electron_integration</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_electron_integration">fix_modify AtC extrinsic electron_integration</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)> <br> +<p>fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)> <br/> +</p> <ul> -<li>integration_type (string) = explicit | implicit | steady <br> -</li></ul> -<p> -num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration<h2><a class="anchor" name="examples"> +<li>integration_type (string) = explicit | implicit | steady <br/> +</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> -<code> fix_modify AtC extrinsic electron_integration implicit </code> <br> - <code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br> -<h2><a class="anchor" name="description"> +<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> -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.<h2><a class="anchor" name="restrictions"> +<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> -For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br> - <h2><a class="anchor" name="default"> +<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> +<h2><a class="anchor" id="default"> default</a></h2> -implicit<br> - subcycle_steps = 1 <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>implicit<br/> + subcycle_steps = 1 </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_equilibrium_start.html b/doc/USER/atc/man_equilibrium_start.html index 5aa645df6e7602929329594010da99645bffd747..3723cf98bf36d1bca05d04c3735f6e9a3209a2fd 100644 --- a/doc/USER/atc/man_equilibrium_start.html +++ b/doc/USER/atc/man_equilibrium_start.html @@ -1,24 +1,50 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer equilibrium_start</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_equilibrium_start">fix_modify AtC transfer equilibrium_start</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC equilibrium_start</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer equilibrium_start <on|off><h2><a class="anchor" name="examples"> +<p>fix_modify AtC equilibrium_start <on|off></p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify atc transfer equilibrium_start on </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify atc equilibrium_start on </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.<h2><a class="anchor" name="restrictions"> +<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> -only needed before filtering is begun<h2><a class="anchor" name="related"> +<p>only needed before filtering is begun</p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_time_filter.html">fix_modify AtC transfer filter</a><h2><a class="anchor" name="default"> +<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> -on <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>on </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_extrinsic_exchange.html b/doc/USER/atc/man_extrinsic_exchange.html index f8337a7cc94fd40e967cdbab16c2a8d04f93ec6f..8f6533ad646beca2b91ad6415f23b6d0c187933a 100644 --- a/doc/USER/atc/man_extrinsic_exchange.html +++ b/doc/USER/atc/man_extrinsic_exchange.html @@ -1,24 +1,50 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix_modify AtC extrinsic exchange</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_extrinsic_exchange">fix_modify AtC extrinsic exchange</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC extrinsic exchange <on|off><h2><a class="anchor" name="examples"> +<p>fix_modify AtC extrinsic exchange <on|off></p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC extrinsic exchange on </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify AtC extrinsic exchange on </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -Switches energy exchange between the MD system and electron system on and off<h2><a class="anchor" name="restrictions"> +<p>Switches energy exchange between the MD system and electron system on and off</p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -Only valid for use with two_temperature type of AtC fix.<h2><a class="anchor" name="related"> +<p>Only valid for use with two_temperature type of AtC fix.</p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_fix_atc.html">fix atc command</a><h2><a class="anchor" name="default"> +<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p> +<h2><a class="anchor" id="default"> default</a></h2> -on <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>on </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_filter_scale.html b/doc/USER/atc/man_filter_scale.html index 606c41f17ab4f7a48747118ecdc058bca0da0f95..975f87e9499be3d210da661bff02dfb556141eae 100644 --- a/doc/USER/atc/man_filter_scale.html +++ b/doc/USER/atc/man_filter_scale.html @@ -1,28 +1,55 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer filter scale</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_filter_scale">fix_modify AtC transfer filter scale</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC filter scale</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer filter scale <scale> <br> +<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" name="examples"> +<li>scale (real) = characteristic time scale of the filter <br/> +</li> +</ul> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC transfer filter scale 10.0 </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify AtC filter scale 10.0 </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -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 <h2><a class="anchor" name="restrictions"> +<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> -only for be used with specific transfers: thermal, two_temperature<h2><a class="anchor" name="related"> +<p>only for be used with specific transfers: thermal, two_temperature</p> +<h2><a class="anchor" id="related"> related</a></h2> -<a class="el" href="man_time_filter.html">fix_modify AtC transfer filter</a><h2><a class="anchor" name="default"> +<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> -0. <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>0. </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_fix_atc.html b/doc/USER/atc/man_fix_atc.html index f30b50349c23834861d894d1bd8ccec7bac358e4..d6076a091a73e60810f204fcd23a5013b2e89b0f 100644 --- a/doc/USER/atc/man_fix_atc.html +++ b/doc/USER/atc/man_fix_atc.html @@ -1,119 +1,255 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix atc command</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_fix_atc">fix atc command</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix AtC transfer <type> <parameter_file><ul> -<li>type<br> - = thermal : thermal coupling with fields: temperature <br> - = two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br> - = hardy : Hardy on-the-fly post-processing (see "related" section for possible fields) <br> -</li><li>parameter_file = name of the file with material parameters. <br> - note: hardy does not require a parameter file </li></ul> -<h2><a class="anchor" name="examples"> +<p>fix <fixID> <group> atc <type> <parameter_file></p> +<ul> +<li>fixID = name of fix</li> +<li>group = name of group fix is to be applied</li> +<li>type<br/> + = thermal : thermal coupling with fields: temperature <br/> + = two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br/> + = hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) <br/> + = field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) <br/> +</li> +<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> -<code> fix_modify AtC transfer thermal Ar_thermal.dat </code> <br> - <code> fix_modify AtC transfer hardy </code> <h2><a class="anchor" name="description"> +<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> -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 Hardy/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> -The following coupling example is typical, but non-exhaustive:<br> -<p> -<code> # ... commands to create and initialize the MD system <br> -</code><p> -<code> # initial fix to designate coupling type and group to apply it to <br> - # tag group physics material_file <br> - fix AtC internal atc thermal Ar_thermal.mat<br> - <br> - # create a uniform 12 x 2 x 2 mesh that covers region contain the group <br> - # nx ny nz region periodicity <br> - fix_modify AtC fem create mesh 12 2 2 mdRegion f p p<br> - <br> - # specify the control method for the type of coupling <br> - # physics control_type <br> - fix_modify AtC transfer thermal control flux <br> - <br> - # specify the initial values for the empirical field "temperature" <br> - # field node_group value <br> - fix_modify AtC transfer initial temperature all 30.<br> - <br> - # create an output stream for nodal fields <br> - # filename output_frequency <br> - fix_modify AtC transfer output atc_fe_output 100<br> - <br> -</code><p> -<code> run 1000 <br> - </code><p> -likewise for this post-processing example: <br> -<p> -<code> # ... commands to create and initialize the MD system <br> -</code><p> -<code> # initial fix to designate post-processing and the group to apply it to <br> - # no material file is allowed nor required <br> - fix AtC internal atc hardy <br> - <br> - # create a uniform 1 x 1 x 1 mesh that covers region contain the group <br> - # with periodicity this effectively creats a system average <br> - fix_modify AtC fem create mesh 1 1 1 box p p p <br> -<br> - # change from default lagrangian map to eulerian <br> - # refreshed every 100 steps <br> - fix_modify AtC atom_element_map eulerian 100 <br> - <br> - # start with no field defined <br> - fix_modify AtC transfer fields none <br> - <br> - # add mass density, potential energy density, stress and temperature <br> - fix_modify AtC transfer fields add density energy stress temperature <br> -<br> - # create an output stream for nodal fields <br> - # filename output_frequency <br> - fix_modify AtC transfer output nvtFE 100 text <br> -</code><p> -<code> run 1000 <br> - </code><p> -Note coupling and post-processing can be combined in the same simulations using separate fixes. <br> - For detailed exposition of the theory and algorithms please see:<br> +<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> +<p><code> # ... commands to create and initialize the MD system <br/> +</code></p> +<p><code> # initial fix to designate coupling type and group to apply it to <br/> + # tag group physics material_file <br/> + fix AtC internal atc thermal Ar_thermal.mat<br/> + <br/> + # create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/> + # nx ny nz region periodicity <br/> + fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/> + <br/> + # specify the control method for the type of coupling <br/> + # physics control_type <br/> + fix_modify AtC thermal control flux <br/> + <br/> + # specify the initial values for the empirical field "temperature" <br/> + # field node_group value <br/> + fix_modify AtC initial temperature all 30.<br/> + <br/> + # create an output stream for nodal fields <br/> + # filename output_frequency <br/> + fix_modify AtC output atc_fe_output 100<br/> + <br/> +</code></p> +<p><code> run 1000 <br/> + </code></p> +<p>likewise for this post-processing example: <br/> +</p> +<p><code> # ... commands to create and initialize the MD system <br/> +</code></p> +<p><code> # initial fix to designate post-processing and the group to apply it to <br/> + # no material file is allowed nor required <br/> + fix AtC internal atc hardy <br/> + <br/> + # for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/> + fix AtC kernel quartic_sphere 10.0 <br/> + <br/> + # create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/> + # with periodicity this effectively creats a system average <br/> + fix_modify AtC mesh create 1 1 1 box p p p <br/> +<br/> + # change from default lagrangian map to eulerian <br/> + # refreshed every 100 steps <br/> + fix_modify AtC atom_element_map eulerian 100 <br/> + <br/> + # start with no field defined <br/> + # add mass density, potential energy density, stress and temperature <br/> + fix_modify AtC fields add density energy stress temperature <br/> +<br/> + # create an output stream for nodal fields <br/> + # filename output_frequency <br/> + fix_modify AtC output nvtFE 100 text <br/> +</code></p> +<p><code> run 1000 <br/> + </code></p> +<p>the mesh's linear interpolation functions can be used as the localization function <br/> + by using the field option: <br/> +</p> +<p><code> fix AtC internal atc field <br/> + <br/> + fix_modify AtC mesh create 1 1 1 box p p p <br/> +<br/> + ... <br/> +<br/> + </code></p> +<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/> + For detailed exposition of the theory and algorithms please see:<br/> +</p> <ul> -<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.</li><li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319</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.<h2><a class="anchor" name="restrictions"> +<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/> +</li> +<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/> +</li> +<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/> +</li> +<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/> +</li> +<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/> +</li> +<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/> +</li> +<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/> +</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> -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> -Currently,<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" name="related"> +<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> -fix_modify commands for setup: <br> +<p>fix_modify commands for setup: <br/> +</p> <ul> -<li><a class="el" href="man_fem_mesh.html">fix_modify AtC fem create mesh</a></li><li><a class="el" href="man_mesh_nodeset.html">fix_modify AtC mesh create_nodeset</a></li><li><a class="el" href="man_mesh_faceset.html">fix_modify AtC mesh create_faceset</a></li><li><a class="el" href="man_mesh_elemset.html">fix_modify AtC mesh create_elementset</a></li><li><a class="el" href="man_transfer_internal.html">fix_modify AtC transfer internal</a></li><li><a class="el" href="man_transfer_boundary.html">fix_modify AtC transfer boundary</a></li><li><a class="el" href="man_internal_quadrature.html">fix_modify AtC transfer internal_quadrature</a></li><li><a class="el" href="man_time_integration.html">fix_modify AtC transfer pmfc</a></li><li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li></ul> -<p> -fix_modify commands for boundary and initial conditions:<br> +<li><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a></li> +<li><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li> +<li><a class="el" href="man_mesh_read.html">fix_modify AtC mesh read</a></li> +<li><a class="el" href="man_mesh_write.html">fix_modify AtC mesh write</a></li> +<li><a class="el" href="man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li> +<li><a class="el" href="man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li> +<li><a class="el" href="man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li> +<li><a class="el" href="man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li> +<li><a class="el" href="man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li> +<li><a class="el" href="man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li> +<li><a class="el" href="man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li> +<li><a class="el" href="man_boundary.html">fix_modify AtC boundary</a></li> +<li><a class="el" href="man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li> +<li><a class="el" href="man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li> +<li><a class="el" href="man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li> +<li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li> +<li><a class="el" href="man_internal_element_set.html">fix_modify AtC internal_element_set</a></li> +<li><a class="el" href="man_decomposition.html">fix_modify AtC decomposition</a></li> +</ul> +<p>fix_modify commands for boundary and initial conditions:<br/> +</p> <ul> -<li><a class="el" href="man_initial.html">fix_modify AtC transfer initial</a></li><li><a class="el" href="man_fix_nodes.html">fix_modify AtC transfer fix</a></li><li><a class="el" href="man_unfix_nodes.html">fix_modify AtC transfer unfix</a></li><li><a class="el" href="man_fix_flux.html">fix_modify AtC transfer fix_flux</a></li><li><a class="el" href="man_unfix_flux.html">fix_modify AtC transfer unfix_flux</a></li><li><a class="el" href="man_source.html">fix_modify AtC transfer source</a></li><li><a class="el" href="man_remove_source.html">fix_modify AtC transfer remove_source</a></li></ul> -<p> -fix_modify commands for control and filtering: <br> +<li><a class="el" href="man_initial.html">fix_modify AtC initial</a></li> +<li><a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a></li> +<li><a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a></li> +<li><a class="el" href="man_fix_flux.html">fix_modify AtC fix_flux</a></li> +<li><a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a></li> +<li><a class="el" href="man_source.html">fix_modify AtC source</a></li> +<li><a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a></li> +</ul> +<p>fix_modify commands for control and filtering: <br/> +</p> <ul> -<li><a class="el" href="man_thermal_control.html">fix_modify AtC transfer thermal control</a></li><li><a class="el" href="man_time_filter.html">fix_modify AtC transfer filter</a></li><li><a class="el" href="man_filter_scale.html">fix_modify AtC transfer filter scale</a></li><li><a class="el" href="man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</a></li><li><a class="el" href="man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li></ul> -<p> -fix_modify commands for output: <br> +<li><a class="el" href="man_control.html">fix_modify AtC control</a></li> +<li><a class="el" href="man_control_thermal.html">fix_modify AtC control thermal</a></li> +<li><a class="el" href="man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li> +<li><a class="el" href="man_control_momentum.html">fix_modify AtC control momentum</a></li> +<li><a class="el" href="man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li> +<li><a class="el" href="man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li> +<li><a class="el" href="man_mask_direction.html">fix_modify AtC control mask_direction</a></li> +<li><a class="el" href="man_time_filter.html">fix_modify AtC filter</a></li> +<li><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></li> +<li><a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></li> +<li><a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li> +<li><a class="el" href="man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li> +<li>man_charge_control</li> +<li><a class="el" href="man_poisson_solver.html">fix_modify AtC poisson_solver</a></li> +</ul> +<p>fix_modify commands for output: <br/> +</p> <ul> -<li><a class="el" href="man_transfer_output.html">fix_modify AtC transfer output</a></li><li><a class="el" href="man_transfer_atomic_output.html">fix_modify AtC transfer atomic_output</a></li><li><a class="el" href="man_mesh_output.html">fix_modify AtC mesh output</a></li><li><a class="el" href="man_write_restart.html">fix_modify AtC transfer write_restart</a></li><li><a class="el" href="man_read_restart.html">fix_modify AtC transfer read_restart</a></li></ul> -<p> -fix_modify commands for post-processing: <br> +<li><a class="el" href="man_output.html">fix_modify AtC output</a></li> +<li><a class="el" href="man_output_nodeset.html">fix_modify AtC output nodeset</a></li> +<li><a class="el" href="man_output_elementset.html">fix_modify AtC output elementset</a></li> +<li><a class="el" href="man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li> +<li><a class="el" href="man_contour_integral.html">fix_modify AtC output contour_integral</a></li> +<li><a class="el" href="man_mesh_output.html">fix_modify AtC mesh output</a></li> +<li><a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a></li> +<li><a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a></li> +</ul> +<p>fix_modify commands for post-processing: <br/> +</p> <ul> -<li><a class="el" href="man_hardy_fields.html">fix_modify AtC transfer fields</a></li><li><a class="el" href="man_hardy_gradients.html">fix_modify AtC transfer gradients</a></li><li><a class="el" href="man_hardy_rates.html">fix_modify AtC transfer rates</a></li><li><a class="el" href="man_hardy_computes.html">fix_modify AtC transfer computes</a></li><li><a class="el" href="man_hardy_set.html">fix_modify AtC set</a></li><li><a class="el" href="man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</a></li><li><a class="el" href="man_boundary_integral.html">fix_modify AtC boundary_integral</a></li><li><a class="el" href="man_contour_integral.html">fix_modify AtC contour_integral</a></li></ul> -<p> -miscellaneous fix_modify commands: <br> +<li><a class="el" href="man_hardy_kernel.html">fix_modify AtC kernel</a></li> +<li><a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li> +<li><a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a></li> +<li><a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a></li> +<li><a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a></li> +<li><a class="el" href="man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li> +<li><a class="el" href="man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li> +<li><a class="el" href="man_sample_frequency.html">fix_modify AtC sample_frequency</a></li> +<li><a class="el" href="man_set.html">fix_modify AtC set</a></li> +</ul> +<p>miscellaneous fix_modify commands: <br/> +</p> <ul> -<li><a class="el" href="man_atom_element_map.html">fix_modify AtC transfer atom_element_map</a></li><li><a class="el" href="man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</a></li></ul> -<p> -Note: a set of example input files with the attendant material files are included with this package <h2><a class="anchor" name="default"> +<li><a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a></li> +<li><a class="el" href="man_atom_weight.html">fix_modify AtC atom_weight</a></li> +<li><a class="el" href="man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li> +<li><a class="el" href="man_reset_time.html">fix_modify AtC reset_time</a></li> +<li><a class="el" href="man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li> +<li><a class="el" href="man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li> +<li><a class="el" href="man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li> +<li><a class="el" href="man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li> +<li><a class="el" href="man_mass_matrix.html">fix_modify AtC mass_matrix</a></li> +<li><a class="el" href="man_material.html">fix_modify AtC material</a></li> +<li><a class="el" href="man_atomic_charge.html">fix_modify AtC atomic_charge</a></li> +<li><a class="el" href="man_source_integration.html">fix_modify AtC source_integration</a></li> +<li><a class="el" href="man_temperature_definition.html">fix_modify AtC temperature_definition</a></li> +<li><a class="el" href="man_track_displacement.html">fix_modify AtC track_displacement</a></li> +<li><a class="el" href="man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li> +<li><a class="el" href="man_add_species.html">fix_modify AtC add_species</a></li> +<li><a class="el" href="man_add_molecule.html">fix_modify AtC add_molecule</a></li> +<li><a class="el" href="man_remove_species.html">fix_modify AtC remove_species</a></li> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_fix_flux.html b/doc/USER/atc/man_fix_flux.html index 44fdd73483e7ac464daf1a0e1ed8a9c61c17dff4..d8369a878533909d87a5695b7b8bc17186c4d537 100644 --- a/doc/USER/atc/man_fix_flux.html +++ b/doc/USER/atc/man_fix_flux.html @@ -1,26 +1,53 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer fix_flux</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_fix_flux">fix_modify AtC transfer fix_flux</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC fix_flux</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer fix_flux <field> <face_set> <value | function><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" name="examples"> +<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> -<code> fix_modify atc transfer fix_flux temperature faceSet 10.0 </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -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. <h2><a class="anchor" name="restrictions"> +<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> -Only normal fluxes (Neumann data) can be prescribed. <h2><a class="anchor" name="related"> +<p>Only normal fluxes (Neumann data) can be prescribed. </p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_unfix_flux.html">fix_modify AtC transfer unfix_flux</a> <h2><a class="anchor" name="default"> +<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> -<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_fix_nodes.html b/doc/USER/atc/man_fix_nodes.html index 788e40d75881d3144f1b2aa7687336502e882aeb..cf5c93590a2f561755953ffc56108911d1e13e4c 100644 --- a/doc/USER/atc/man_fix_nodes.html +++ b/doc/USER/atc/man_fix_nodes.html @@ -1,27 +1,56 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer fix</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_fix_nodes">fix_modify AtC transfer fix</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC fix</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer fix <field> <nodeset> <constant | function><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" name="examples"> +<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> -<code> fix_modify AtC transfer fix temperature groupNAME 10. </code> <br> - <code> fix_modify AtC transfer fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br> - <h2><a class="anchor" name="description"> +<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> -Creates a constraint on the values of the specified field at specified nodes. <h2><a class="anchor" name="restrictions"> +<p>Creates a constraint on the values of the specified field at specified nodes. </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -keyword 'all' reserved in nodeset name <h2><a class="anchor" name="related"> +<p>keyword 'all' reserved in nodeset name </p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_unfix_nodes.html">fix_modify AtC transfer unfix</a> <h2><a class="anchor" name="default"> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_computes.html b/doc/USER/atc/man_hardy_computes.html index 5eba042b99d41cf658e8d82983d35168e1e3f768..c16550742b89e24e77917fbbe5322276201d3fb0 100644 --- a/doc/USER/atc/man_hardy_computes.html +++ b/doc/USER/atc/man_hardy_computes.html @@ -1,38 +1,67 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer computes</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_hardy_computes">fix_modify AtC transfer computes</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC computes</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer computes <add | delete> [per-atom compute id] <volume | number> <br> +<p>fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number> <br/> +</p> <ul> -<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br> -</li><li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br> -</li><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" name="examples"> +<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br/> +</li> +<li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br/> +</li> +<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> -<code> compute virial all stress/atom </code> <br> - <code> fix_modify AtC transfer computes add virial volume </code> <br> - <code> fix_modify AtC transfer computes delete virial </code> <br> - <br> - <code> compute centrosymmetry all centro/atom </code> <br> - <code> fix_modify AtC transfer computes add centrosymmetry number </code> <br> - <h2><a class="anchor" name="description"> +<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/> + <br/> + <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> -Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br> - <h2><a class="anchor" name="restrictions"> +<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/> + </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br> - Per-atom compute must be specified before corresponding continuum field can be requested <br> - <h2><a class="anchor" name="related"> +<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/> + Per-atom compute must be specified before corresponding continuum field can be requested <br/> + </p> +<h2><a class="anchor" id="related"> related</a></h2> -See manual page for compute <h2><a class="anchor" name="default"> +<p>See manual page for compute </p> +<h2><a class="anchor" id="default"> default</a></h2> -No defaults exist for this command <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<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 <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> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_fields.html b/doc/USER/atc/man_hardy_fields.html index fd23662f85a88f545621d11df70046c50f554b48..1f55fd5e3702cb8cbaa4f3f59e4ab7e2ebf3657f 100644 --- a/doc/USER/atc/man_hardy_fields.html +++ b/doc/USER/atc/man_hardy_fields.html @@ -1,46 +1,83 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer fields</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_hardy_fields">fix_modify AtC transfer fields</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC fields</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer fields <all | none> <br> - fix_modify AtC transfer fields <add | delete> <list_of_fields> <br> +<p>fix_modify AtC fields <all | none> <br/> + fix_modify AtC fields <add | delete> <list_of_fields> <br/> +</p> <ul> -<li>all | none (keyword) = output all or no fields <br> -</li><li>add | delete (keyword) = add or delete the listed output fields <br> -</li><li>fields (keyword) = <br> - density : mass per unit volume <br> - displacement : displacement vector <br> - momentum : momentum per unit volume <br> - velocity : defined by momentum divided by density <br> - projected_velocity : simple kernel estimation of atomic velocities <br> - temperature : temperature derived from the relative atomic kinetic energy (as done by Hardy) <br> - kinetic_temperature : temperature derived from the full kinetic energy <br> - energy : total energy (potential + kinetic) per unit volume <br> - number_density : simple kernel estimation of number of atoms per unit volume <br> - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br> - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br> - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br> - </li></ul> -<h2><a class="anchor" name="examples"> +<li>all | none (keyword) = output all or no fields <br/> +</li> +<li>add | delete (keyword) = add or delete the listed output fields <br/> +</li> +<li>fields (keyword) = <br/> + density : mass per unit volume <br/> + displacement : displacement vector <br/> + momentum : momentum per unit volume <br/> + velocity : defined by momentum divided by density <br/> + projected_velocity : simple kernel estimation of atomic velocities <br/> + temperature : temperature derived from the relative atomic kinetic energy (as done by ) <br/> + kinetic_temperature : temperature derived from the full kinetic energy <br/> + number_density : simple kernel estimation of number of atoms per unit volume <br/> + stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br/> + transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br/> + heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br/> + potential_energy : potential energy per unit volume <br/> + kinetic_energy : kinetic energy per unit volume <br/> + thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume <br/> + internal_energy : total internal energy (potential + thermal) per unit volume <br/> + energy : total energy (potential + kinetic) per unit volume <br/> + number_density : number of atoms per unit volume <br/> + eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] <br/> + vacancy_concentration: volume fraction of vacancy content <br/> + type_concentration: volume fraction of a specific atom type <br/> + </li> +</ul> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC transfer fields add velocity temperature </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC fields add velocity temperature </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Allows modification of the fields calculated and output by the Hardy transfer class. The commands are cumulative, e.g.<br> - <code> fix_modify AtC transfer fields none </code> <br> - followed by <br> - <code> fix_modify AtC transfer fields add velocity temperature </code> <br> - will only output the velocity and temperature fields. <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer, 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. <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p> +<h2><a class="anchor" id="related"> related</a></h2> -See <a class="el" href="man_hardy_gradients.html">fix_modify AtC transfer gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC transfer rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC transfer computes</a> <h2><a class="anchor" name="default"> +<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> -All fields are output by default <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<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 <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> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_gradients.html b/doc/USER/atc/man_hardy_gradients.html index caeb8b1749bcca910cb8dc7eb089d327afb5af5c..708fecbca1dedd4470e5b6e6e15090b37aec4a48 100644 --- a/doc/USER/atc/man_hardy_gradients.html +++ b/doc/USER/atc/man_hardy_gradients.html @@ -1,30 +1,57 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer gradients</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_hardy_gradients">fix_modify AtC transfer gradients</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC gradients</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer gradients <add | delete> <list_of_fields> <br> +<p>fix_modify AtC gradients <add | delete> <list_of_fields> <br/> +</p> <ul> -<li>add | delete (keyword) = add or delete the calculation of gradients for the listed output fields <br> -</li><li>fields (keyword) = <br> - gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC transfer fields</a></li></ul> -<h2><a class="anchor" name="examples"> +<li>add | delete (keyword) = add or delete the calculation of gradients for the listed output fields <br/> +</li> +<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> -<code> fix_modify AtC transfer gradients add temperature velocity stress </code> <br> - <code> fix_modify AtC transfer gradients delete velocity </code> <br> - <h2><a class="anchor" name="description"> +<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> -Requests calculation and ouput of gradients of the fields from the Hardy 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 transfer atom_element_map</a> ) <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -No gradients are calculated by default <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<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 <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> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_kernel.html b/doc/USER/atc/man_hardy_kernel.html index 20c9410e5cc54dbb4d49f961d31c53df97dd006b..3d81b367dd0e59c39be54580b80069c147d84cf6 100644 --- a/doc/USER/atc/man_hardy_kernel.html +++ b/doc/USER/atc/man_hardy_kernel.html @@ -1,36 +1,65 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix_modify AtC kernel</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_hardy_kernel">fix_modify AtC kernel</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer kernel <type> <parameters><ul> -<li>type (keyword) = mesh, step, cell, cubic_cylinder, cubic_sphere, quartic_cylinder, quartic_sphere <br> -</li><li>parameters :<br> - mesh = none<br> - step = radius (double) <br> - cell = hx, hy, hz (double) or h (double) <br> - cubic_cylinder = radius (double) <br> - cubic_sphere = radius (double) <br> - quartic_cylinder = radius (double) <br> - quartic_sphere = radius (double) <br> - </li></ul> -<h2><a class="anchor" name="examples"> +<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/> +</li> +<li>parameters :<br/> + step = radius (double) <br/> + cell = hx, hy, hz (double) or h (double) <br/> + cubic_bar = half-width (double) <br/> + cubic_cylinder = radius (double) <br/> + cubic_sphere = radius (double) <br/> + quartic_bar = half-width (double) <br/> + quartic_cylinder = radius (double) <br/> + quartic_sphere = radius (double) <br/> + </li> +</ul> +<h2><a class="anchor" id="examples"> examples</a></h2> -fix_modify AtC transfer kernel cell 1.0 1.0 1.0 <h2><a class="anchor" name="description"> +<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" name="restrictions"> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -Must be used with the hardy AtC transfer <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> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy AtC fix <br/> + For bar kernel types, half-width oriented along x-direction <br/> + For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/> + ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -Default to the mesh based kernel <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>No default </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_on_the_fly.html b/doc/USER/atc/man_hardy_on_the_fly.html index 4d9645f1af4927aedd8d4e12689347b5e3bfca1e..d140cf6840e290a81e312aab76129992cf5ca5ed 100644 --- a/doc/USER/atc/man_hardy_on_the_fly.html +++ b/doc/USER/atc/man_hardy_on_the_fly.html @@ -1,34 +1,60 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer on_the_fly</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_hardy_on_the_fly">fix_modify AtC transfer on_the_fly</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC on_the_fly</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC transfer on_the_fly <bond | kernel> <optional on | off> <br> +<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> <ul> -<li>bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br> -</li><li>on | off (keyword) = activate or discontinue on-the-fly mode <br> -</li></ul> -<h2><a class="anchor" name="examples"> +<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/> + </li> +</ul> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC transfer on_the_fly bond on </code> <br> - <code> fix_modify AtC transfer on_the_fly kernel </code> <br> - <code> fix_modify AtC transfer on_the_fly kernel off </code> <br> - <h2><a class="anchor" name="description"> +<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> -Overrides normal mode of pre-calculating and storing bond pair-to-node and kernel atom-to-node matrices. If activated, will calculate elements of these 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 specified matrix. Can be deactivated using off flag. <br> - <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -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 elements. If this allocation fails, on-the-fly is activated. <br> - <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<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> +<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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_hardy_rates.html b/doc/USER/atc/man_hardy_rates.html index f8d002d32fabb408f98f06b79306fa320cbd91d1..ab0315cb65b179cf01b60309711d2d9c2ba87942 100644 --- a/doc/USER/atc/man_hardy_rates.html +++ b/doc/USER/atc/man_hardy_rates.html @@ -1,31 +1,58 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer rates</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_hardy_rates">fix_modify AtC transfer rates</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC rates</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer rates <add | delete> <list_of_fields> <br> +<p>fix_modify AtC rates <add | delete> <list_of_fields> <br/> +</p> <ul> -<li>add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields <br> -</li><li>fields (keyword) = <br> - rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC transfer fields</a></li></ul> -<h2><a class="anchor" name="examples"> +<li>add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields <br/> +</li> +<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> -<code> fix_modify AtC transfer rates add temperature velocity stress </code> <br> - <code> fix_modify AtC transfer rates delete stress </code> <br> - <h2><a class="anchor" name="description"> +<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> -Requests calculation and ouput of rates (time derivatives) of the fields from the Hardy transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC transfer atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br> - <h2><a class="anchor" name="restrictions"> +<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> -Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related"> +<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -No rates are calculated by default <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<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 <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> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_initial.html b/doc/USER/atc/man_initial.html index 73438c9252e1463506e7504655791cc02d8d8cbe..c0a0be38523ed357b7806b006574cd5a3f08e5c0 100644 --- a/doc/USER/atc/man_initial.html +++ b/doc/USER/atc/man_initial.html @@ -1,25 +1,51 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer initial</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_initial">fix_modify AtC transfer initial</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC initial</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer initial <field> <nodeset> <constant | function><ul> -<li><field> = field name valid for type of physics, temperature | electron_temperature</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" name="examples"> +<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> -<code> fix_modify atc transfer initial temperature groupNAME 10. </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Sets the initial values for the specified field at the specified nodes. <h2><a class="anchor" name="restrictions"> +<p>Sets the initial values for the specified field at the specified nodes. </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -keyword 'all' reserved in nodeset name <h2><a class="anchor" name="related"> -related</a></h2> -see <a class="el" href="man_transfer_internal.html">fix_modify AtC transfer internal</a> <h2><a class="anchor" name="default"> +<p>keyword 'all' reserved in nodeset name </p> +<h2><a class="anchor" id="default"> default</a></h2> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_internal_quadrature.html b/doc/USER/atc/man_internal_quadrature.html index beff89bddb9a32bd8f2edd413737b382c0e78e11..172187c2982093bd0109f01ef7d1922af38403f2 100644 --- a/doc/USER/atc/man_internal_quadrature.html +++ b/doc/USER/atc/man_internal_quadrature.html @@ -1,23 +1,50 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer internal_quadrature</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_internal_quadrature">fix_modify AtC transfer internal_quadrature</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC internal_quadrature</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify atc transfer internal_quadrature < on | off > <h2><a class="anchor" name="examples"> +<p>fix_modify atc internal_quadrature <on | off> [region] </p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify atc transfer internal_quadrature off </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify atc internal_quadrature off </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Command 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. <h2><a class="anchor" name="restrictions"> +<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> +<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" name="related"> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -on <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>on </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_mesh_delete_elements.html b/doc/USER/atc/man_mesh_delete_elements.html index a4f025eedc496a47e3c713f26d98344d4362dd87..cc269c8e651d7c1ade24c3b38df1e8bcebcb7907 100644 --- a/doc/USER/atc/man_mesh_delete_elements.html +++ b/doc/USER/atc/man_mesh_delete_elements.html @@ -1,25 +1,50 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix_modify AtC mesh delete_elements</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_mesh_delete_elements">fix_modify AtC mesh delete_elements</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<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> -fix_modify AtC mesh delete_elements <element_set><ul> -<li><element_set> = name of an element set </li></ul> -<h2><a class="anchor" name="examples"> +<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> -<code> fix_modify AtC delete_elements gap </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC delete_elements gap </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Deletes a group of elements from the mesh. <h2><a class="anchor" name="restrictions"> +<p>Deletes a group of elements from the mesh. </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -<h2><a class="anchor" name="related"> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_mesh_output.html b/doc/USER/atc/man_mesh_output.html index 5e336fb5ae6ad0698a979e7230f9dff531eeca76..be1b4c194f4d83fc6bd273a7a621e8ed782c55d2 100644 --- a/doc/USER/atc/man_mesh_output.html +++ b/doc/USER/atc/man_mesh_output.html @@ -1,24 +1,49 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <title>ATC: fix_modify AtC mesh output</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_mesh_output">fix_modify AtC mesh output</a></h1><h2><a class="anchor" name="syntax"> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC mesh output <file_prefix> <h2><a class="anchor" name="examples"> +<p>fix_modify AtC mesh output <file_prefix> </p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC mesh output meshData </code> <br> - <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC mesh output meshData </code> <br/> + </p> +<h2><a class="anchor" id="description"> description</a></h2> -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. <h2><a class="anchor" name="restrictions"> +<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> -none <h2><a class="anchor" name="related"> +<p>none </p> +<h2><a class="anchor" id="related"> related</a></h2> -<h2><a class="anchor" name="default"> +<h2><a class="anchor" id="default"> default</a></h2> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_read_restart.html b/doc/USER/atc/man_read_restart.html index c7c9a35f4f89ef9d14c95cacd87353002d1e95af..96168fccc769fce0a7d6e15c21e024f61a2500aa 100644 --- a/doc/USER/atc/man_read_restart.html +++ b/doc/USER/atc/man_read_restart.html @@ -1,25 +1,51 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer read_restart</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_read_restart">fix_modify AtC transfer read_restart</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC read_restart</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer read_restart [file_name] <br> - <h2><a class="anchor" name="examples"> +<p>fix_modify AtC read_restart [file_name] <br/> + </p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC transfer read_restart ATC_state </code> <br> - <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC read_restart ATC_state </code> <br/> + </p> +<h2><a class="anchor" id="description"> description</a></h2> -Reads the current state of the fields from a named text-based restart file. <h2><a class="anchor" name="restrictions"> +<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> -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. <h2><a class="anchor" name="related"> +<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> -see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC transfer write_restart</a> <h2><a class="anchor" name="default"> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_remove_source.html b/doc/USER/atc/man_remove_source.html index 7678d4ccef4acab602a20a7bb567bd79117596a2..d1d249eb76b0a7ab764f04ee472bb23d44a9afbb 100644 --- a/doc/USER/atc/man_remove_source.html +++ b/doc/USER/atc/man_remove_source.html @@ -1,25 +1,52 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer remove_source</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_remove_source">fix_modify AtC transfer remove_source</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC remove_source</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer remove_source <field> <element_set><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" name="examples"> +<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> -<code> fix_modify atc transfer remove_source temperature groupNAME </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify atc remove_source temperature groupNAME </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Remove a domain source. <h2><a class="anchor" name="restrictions"> +<p>Remove a domain source. </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -keyword 'all' reserved in element_set name <h2><a class="anchor" name="related"> +<p>keyword 'all' reserved in element_set name </p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_source.html">fix_modify AtC transfer source</a> <h2><a class="anchor" name="default"> +<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p> +<h2><a class="anchor" id="default"> default</a></h2> -<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_source.html b/doc/USER/atc/man_source.html index d8070635c6039a7d9d0924ab7204d175d3abccc2..833b2a866f4d28ad552ea2c257022dd0a77baacc 100644 --- a/doc/USER/atc/man_source.html +++ b/doc/USER/atc/man_source.html @@ -1,25 +1,53 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer source</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_source">fix_modify AtC transfer source</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC source</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer source <field> <element_set> <value | function><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" name="examples"> +<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> -<code> fix_modify atc transfer source temperature middle temporal_ramp 10. 0. </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -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. <h2><a class="anchor" name="restrictions"> +<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> -keyword 'all' reserved in element_set name <h2><a class="anchor" name="related"> +<p>keyword 'all' reserved in element_set name </p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_remove_source.html">fix_modify AtC transfer remove_source</a> <h2><a class="anchor" name="default"> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_time_filter.html b/doc/USER/atc/man_time_filter.html index 1d7777324262dcce1e1aa2c8d2b278a763aec222..ec70fed871761cfb327546273ea249c471bc98ba 100644 --- a/doc/USER/atc/man_time_filter.html +++ b/doc/USER/atc/man_time_filter.html @@ -1,29 +1,57 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer filter</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_time_filter">fix_modify AtC transfer filter</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC filter</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer filter <on | off | equilibrate> <br> +<p>fix_modify AtC filter <on | off | equilibrate> <br/> +</p> <ul> -<li>on | off (keyword) = turns filter on or off<br> -</li><li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li></ul> -<h2><a class="anchor" name="examples"> +<li>on | off (keyword) = turns filter on or off<br/> +</li> +<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li> +</ul> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify atc transfer filter on </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify atc transfer filter on </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -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<h2><a class="anchor" name="restrictions"> +<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> -only for be used with specific transfers: thermal, two_temperature<h2><a class="anchor" name="related"> +<p>only for be used with specific transfers: thermal, two_temperature</p> +<h2><a class="anchor" id="related"> related</a></h2> -<a class="el" href="man_filter_scale.html">fix_modify AtC transfer filter scale</a> <br> - <a class="el" href="man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</a><h2><a class="anchor" name="default"> +<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> -off <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>off </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_unfix_flux.html b/doc/USER/atc/man_unfix_flux.html index cdea61b8fe3556eaeb2f88f2d5c4c77b9a7fe2a7..b2a19a7fd0282edf2576a43777a89339c9d11a4b 100644 --- a/doc/USER/atc/man_unfix_flux.html +++ b/doc/USER/atc/man_unfix_flux.html @@ -1,26 +1,52 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer unfix_flux</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_unfix_flux">fix_modify AtC transfer unfix_flux</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC unfix_flux</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer fix_flux <field> <face_set> <value | function><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" name="examples"> +<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> -<code> fix_modify atc transfer unfix_flux temperature faceSet </code> <br> -<h2><a class="anchor" name="description"> +<p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/> +</p> +<h2><a class="anchor" id="description"> description</a></h2> -Command for removing prescribed normal fluxes e.g. heat_flux, stress. <h2><a class="anchor" name="restrictions"> +<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" name="related"> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_unfix_flux.html">fix_modify AtC transfer unfix_flux</a> <h2><a class="anchor" name="default"> +<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> -<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_unfix_nodes.html b/doc/USER/atc/man_unfix_nodes.html index 7a7d77c236e3ab0919a43cc9ca90795907c61169..498d549f9eb6dc1a34532f1a35e502ae483181c5 100644 --- a/doc/USER/atc/man_unfix_nodes.html +++ b/doc/USER/atc/man_unfix_nodes.html @@ -1,25 +1,53 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer unfix</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_unfix_nodes">fix_modify AtC transfer unfix</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC unfix</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer unfix <field> <nodeset><ul> -<li><field> = field name valid for type of physics</li><li><nodeset> = name of set of nodes </li></ul> -<h2><a class="anchor" name="examples"> +<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> -<code> fix_modify AtC transfer unfix temperature groupNAME </code> <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC unfix temperature groupNAME </code> </p> +<h2><a class="anchor" id="description"> description</a></h2> -Removes constraint on field values for specified nodes. <h2><a class="anchor" name="restrictions"> +<p>Removes constraint on field values for specified nodes. </p> +<h2><a class="anchor" id="restrictions"> restrictions</a></h2> -keyword 'all' reserved in nodeset name <h2><a class="anchor" name="related"> +<p>keyword 'all' reserved in nodeset name </p> +<h2><a class="anchor" id="related"> related</a></h2> -see <a class="el" href="man_fix_nodes.html">fix_modify AtC transfer fix</a> <h2><a class="anchor" name="default"> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html> diff --git a/doc/USER/atc/man_write_restart.html b/doc/USER/atc/man_write_restart.html index bd92e3e9065a98f903b2f0265f81c9b767160357..6ea350d5e859a3985dce72e47445c9cc583024f0 100644 --- a/doc/USER/atc/man_write_restart.html +++ b/doc/USER/atc/man_write_restart.html @@ -1,25 +1,51 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> -<title>ATC: fix_modify AtC transfer write_restart</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_write_restart">fix_modify AtC transfer write_restart</a></h1><h2><a class="anchor" name="syntax"> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<title>ATC: fix_modify AtC write_restart</title> +<link href="tabs.css" rel="stylesheet" type="text/css"/> +<link href="doxygen.css" rel="stylesheet" type="text/css"/> +</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"> + + +<h1><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h1><h2><a class="anchor" id="syntax"> syntax</a></h2> -fix_modify AtC transfer write_restart [file_name] <br> - <h2><a class="anchor" name="examples"> +<p>fix_modify AtC write_restart [file_name] <br/> + </p> +<h2><a class="anchor" id="examples"> examples</a></h2> -<code> fix_modify AtC transfer write_restart restart.mydata </code> <br> - <h2><a class="anchor" name="description"> +<p><code> fix_modify AtC write_restart restart.mydata </code> <br/> + </p> +<h2><a class="anchor" id="description"> description</a></h2> -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. <h2><a class="anchor" name="restrictions"> +<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> -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. <h2><a class="anchor" name="related"> +<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> -see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC transfer read_restart</a> <h2><a class="anchor" name="default"> +<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> -none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by +<p>none </p> +</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"> -<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address> +<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address> </body> </html>