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insert new toplevel text into USER-ATC docs, change header levels.

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Axel Kohlmeyer
2018-02-13 12:43:32 +01:00
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<a href="http://lammps.sandia.gov">Website</a>
<a href="../../Section_commands.html#comm">Commands</a>
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USER-AtC Manual
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<hr>
<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/> <p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
</p> </p>
<ul> <ul>
@ -23,21 +37,21 @@ syntax</a></h2>
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/> <li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> group WATERGROUP type 1 2 </code> <br/> <p><code> group WATERGROUP type 1 2 </code> <br/>
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/> <code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Associates a tag with all molecules corresponding to a specified group. <br/> <p>Associates a tag with all molecules corresponding to a specified group. <br/>
</p> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No defaults for this command. </p> <p>No defaults for this command. </p>
</div> </div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp; <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

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<a href="http://lammps.sandia.gov">Website</a>
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USER-AtC Manual
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</div>
<hr>
<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/> <p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
</p> </p>
<ul> <ul>
@ -23,21 +37,21 @@ syntax</a></h2>
<li>&lt;ID&gt; = name of group or type number <br/> <li>&lt;ID&gt; = name of group or type number <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/> <p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/> <code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p> <code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/> <p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
</p> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No defaults for this command. </p> <p>No defaults for this command. </p>
</div> </div>
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<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/> <p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
</p> </p>
<ul> <ul>
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li> <li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p> <p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Cannot change map type after initialization. </p> <p>Cannot change map type after initialization. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>lagrangian </p> <p>lagrangian </p>
</div> </div>
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<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p> <p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
<ul> <ul>
<li>&lt;method&gt; = <br/> <li>&lt;method&gt; = <br/>
@ -24,22 +38,22 @@ syntax</a></h2>
read_in: list of values for atoms are read-in from specified file <br/> read_in: list of values for atoms are read-in from specified file <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/> <p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/> <code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/> <code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p> <p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p> <p>Use of lattice option requires a lattice type and parameter is already specified. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>lattice </p> <p>lattice </p>
</div> </div>
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<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p> <p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
<ul> <ul>
<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li> <li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc compute include atomic_charge </code> </p> <p><code> fix_modify atc compute include atomic_charge </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Determines whether AtC tracks the total charge as a finite element field </p> <p>Determines whether AtC tracks the total charge as a finite element field </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Required for: electrostatics </p> <p>Required for: electrostatics </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>if the atom charge is defined, default is on, otherwise default is off </p> <p>if the atom charge is defined, default is on, otherwise default is off </p>
</div> </div>
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<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p> <p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
<ul> <ul>
<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li> <li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p> <p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p> <p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/> <p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p> <p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p> <p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>prescribed on </p> <p>prescribed on </p>
</div> </div>
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<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p> <p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p>fix_modify AtC boundary_faceset is obndy </p> <p>fix_modify AtC boundary_faceset is obndy </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p> <p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>This is only valid when fe_md_boundary is set to faceset. </p> <p>This is only valid when fe_md_boundary is set to faceset. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p> <p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
<ul> <ul>
<li>field (string) : name of hardy field</li> <li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset </li> <li>name (string) : name of faceset </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/> <p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p> <p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul> <ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li> <li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p> <p><code> fix_modify atc consistent_fe_initialization on </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p> <p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p> <p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Default is off </p> <p>Default is off </p>
</div> </div>
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<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p> <p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
<ul> <ul>
<li>field (string) : name of hardy field</li> <li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset</li> <li>name (string) : name of faceset</li>
<li>axis (string) : x or y or z </li> <li>axis (string) : x or y or z </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/> <p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_control">fix_modify AtC control </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p> <p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
<p><br/> <p><br/>
</p> </p>
@ -34,22 +48,22 @@ syntax</a></h2>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/> <li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/> <p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/> <code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p> <p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for be used with specific controllers : thermal, momentum <br/> <p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p> They are ignored if a lumped solution is requested </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>max_iterations is the number of rows in the matrix<br/> <p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p> tolerance is 1.e-10 </p>
</div> </div>

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<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control momentum none <br/> <p>fix_modify AtC control momentum none <br/>
</p> </p>
<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/> <p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
@ -32,21 +46,21 @@ syntax</a></h2>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/> <li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p>fix_modify AtC control momentum glc_velocity <br/> <p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/> fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only to be used with specific transfers : elastic <br/> <p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p> rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p> <p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
<ul> <ul>
<li>control_type (string) = none | rescale | hoover | flux<br/> <li>control_type (string) = none | rescale | hoover | flux<br/>
@ -34,25 +48,25 @@ syntax</a></h2>
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/> <li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC control thermal none </code> <br/> <p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/> <code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/> <code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/> <code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/> <code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p> <p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/> <p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p> rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none<br/> <p>none<br/>
rescale frequency is 1<br/> rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p> flux boundary_integration_type is interpolate </p>

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<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p> <p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
<ul> <ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/> <li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/> <p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p> <p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for use with thermal physics using the fractional step method. </p> <p>only for use with thermal physics using the fractional step method. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>correction_max_iterations is 20 </p> <p>correction_max_iterations is 20 </p>
</div> </div>
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<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC decomposition &lt;type&gt;</p> <p>fix_modify AtC decomposition &lt;type&gt;</p>
<ul> <ul>
<li>&lt;type&gt; = <br/> <li>&lt;type&gt; = <br/>
@ -20,20 +34,20 @@ syntax</a></h2>
distributed_memory: only owned nodal information on processor <br/> distributed_memory: only owned nodal information on processor <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/> <p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command for assigning the distribution of work and memory for parallel runs. </p> <p>Command for assigning the distribution of work and memory for parallel runs. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p> <p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>replicated_memory </p> <p>replicated_memory </p>
</div> </div>
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<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/> <p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
</p> </p>
<ul> <ul>
@ -20,20 +34,20 @@ syntax</a></h2>
</li> </li>
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li> <li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/> <p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/> <code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/> <p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
</p> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>implicit<br/> <p>implicit<br/>
subcycle_steps = 1 </p> subcycle_steps = 1 </p>
</div> </div>

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<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p> <p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc equilibrium_start on </code> <br/> <p><code> fix_modify atc equilibrium_start on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p> <p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only needed before filtering is begun</p> <p>only needed before filtering is begun</p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p> <p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>on </p> <p>on </p>
</div> </div>
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<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p> <p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC extrinsic exchange on </code> <br/> <p><code> fix_modify AtC extrinsic exchange on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Switches energy exchange between the MD system and electron system on and off</p> <p>Switches energy exchange between the MD system and electron system on and off</p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only valid for use with two_temperature type of AtC fix.</p> <p>Only valid for use with two_temperature type of AtC fix.</p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>on </p> <p>on </p>
</div> </div>
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<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p> <p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/> <p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p> <p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p> <p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see for how to specify the faceset name. </p> <p>see for how to specify the faceset name. </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Interpolate. </p> <p>Interpolate. </p>
</div> </div>
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<h3><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" name="syntax">
syntax</a></h4>
fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul> fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul> <li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
<h2><a class="anchor" name="examples"> <h4><a class="anchor" name="examples">
examples</a></h2> examples</a></h4>
<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description"> <code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h4><a class="anchor" name="description">
description</a></h2> description</a></h4>
Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions"> Creates a uniform mesh in a rectangular region <h4><a class="anchor" name="restrictions">
restrictions</a></h2> restrictions</a></h4>
creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related"> creates only uniform rectangular grids in a rectangular region <h4><a class="anchor" name="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" name="default"> <h4><a class="anchor" name="default">
default</a></h2> default</a></h4>
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<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC filter scale &lt;scale&gt; <br/> <p>fix_modify AtC filter scale &lt;scale&gt; <br/>
</p> </p>
<ul> <ul>
<li>scale (real) = characteristic time scale of the filter <br/> <li>scale (real) = characteristic time scale of the filter <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC filter scale 10.0 </code> <br/> <p><code> fix_modify AtC filter scale 10.0 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p> <p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p> <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"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>0. </p> <p>0. </p>
</div> </div>
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<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/> <p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC filter type exponential </code> <br/> <p><code> fix_modify AtC filter type exponential </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Specifies the type of time filter used. </p> <p>Specifies the type of time filter used. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p> <p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p> <p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No default. </p> <p>No default. </p>
</div> </div>
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<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_fix_atc">fix atc command </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p> <p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p>
<ul> <ul>
<li>fixID = name of fix</li> <li>fixID = name of fix</li>
@ -26,15 +40,15 @@ syntax</a></h2>
<li>parameter_file = name of the file with material parameters. <br/> <li>parameter_file = name of the file with material parameters. <br/>
note: Neither hardy nor field requires a parameter file </li> note: Neither hardy nor field requires a parameter file </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/> <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 two_temperature Ar_ttm.mat </code> <br/>
<code> fix AtC internal atc hardy </code> <br/> <code> fix AtC internal atc hardy </code> <br/>
<code> fix AtC internal atc field </code> <br/> <code> fix AtC internal atc field </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p> <p>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>The following coupling example is typical, but non-exhaustive:<br/>
</p> </p>
@ -122,16 +136,16 @@ description</a></h2>
</li> </li>
</ul> </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> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p> <p>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> <p>Currently,</p>
<ul> <ul>
<li>the coupling is restricted to thermal physics</li> <li>the coupling is restricted to thermal physics</li>
<li>the FE computations are done in serial on each processor.</li> <li>the FE computations are done in serial on each processor.</li>
</ul> </ul>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>fix_modify commands for setup: <br/> <p>fix_modify commands for setup: <br/>
</p> </p>
<ul> <ul>
@ -231,8 +245,8 @@ related</a></h2>
<li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li> <li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
</ul> </ul>
<p>Note: a set of example input files with the attendant material files are included with this package </p> <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"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p> <p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li> <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li> <li>&lt;face_set&gt; = name of set of element faces </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/> <p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only normal fluxes (Neumann data) can be prescribed. </p> <p>Only normal fluxes (Neumann data) can be prescribed. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p> <p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p> <p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics</li> <li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li> <li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li> <li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/> <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/> <code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Creates a constraint on the values of the specified field at specified nodes. </p> <p>Creates a constraint on the values of the specified field at specified nodes. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p> <p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p> <p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/> <p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/>
</p> </p>
<ul> <ul>
@ -23,8 +37,8 @@ syntax</a></h2>
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/> <li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> compute virial all stress/atom </code> <br/> <p><code> compute virial all stress/atom </code> <br/>
<code> fix_modify AtC computes add virial volume </code> <br/> <code> fix_modify AtC computes add virial volume </code> <br/>
<code> fix_modify AtC computes delete virial </code> <br/> <code> fix_modify AtC computes delete virial </code> <br/>
@ -32,20 +46,20 @@ examples</a></h2>
<code> compute centrosymmetry all centro/atom </code> <br/> <code> compute centrosymmetry all centro/atom </code> <br/>
<code> fix_modify AtC computes add centrosymmetry number </code> <br/> <code> fix_modify AtC computes add centrosymmetry number </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/> <p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
</p> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
Per-atom compute must be specified before corresponding continuum field can be requested <br/> Per-atom compute must be specified before corresponding continuum field can be requested <br/>
</p> </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>See manual page for compute </p> <p>See manual page for compute </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No defaults exist for this command </p> <p>No defaults exist for this command </p>
</div> </div>
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<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC fields &lt;all | none&gt; <br/> <p>fix_modify AtC fields &lt;all | none&gt; <br/>
fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/> fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p> </p>
@ -44,24 +58,24 @@ syntax</a></h2>
type_concentration: volume fraction of a specific atom type <br/> type_concentration: volume fraction of a specific atom type <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC fields add velocity temperature </code> </p> <p><code> fix_modify AtC fields add velocity temperature </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/> <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/> <code> fix_modify AtC fields none </code> <br/>
followed by <br/> followed by <br/>
<code> fix_modify AtC fields add velocity temperature </code> <br/> <code> fix_modify AtC fields add velocity temperature </code> <br/>
will only output the velocity and temperature fields. </p> will only output the velocity and temperature fields. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p> <p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p> <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"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>By default, no fields are output </p> <p>By default, no fields are output </p>
</div> </div>
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<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/> <p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p> </p>
<ul> <ul>
@ -21,21 +35,21 @@ syntax</a></h2>
<li>fields (keyword) = <br/> <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> gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/> <p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
<code> fix_modify AtC gradients delete velocity </code> <br/> <code> fix_modify AtC gradients delete velocity </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No gradients are calculated by default </p> <p>No gradients are calculated by default </p>
</div> </div>
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<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p> <p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul> <ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/> <li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@ -28,22 +42,22 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/> quartic_sphere = radius (double) <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/> <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> <code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/> <p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <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/> For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No default </p> <p>No default </p>
</div> </div>
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<h1><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/> <p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/> - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
</p> </p>
@ -20,24 +34,24 @@ syntax</a></h2>
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/> <li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC on_the_fly bond on </code> <br/> <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 </code> <br/>
<code> fix_modify AtC on_the_fly kernel off </code> <br/> <code> fix_modify AtC on_the_fly kernel off </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/> <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/> 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> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/> <p>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> </p>
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<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/> <p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p> </p>
<ul> <ul>
@ -21,22 +35,22 @@ syntax</a></h2>
<li>fields (keyword) = <br/> <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> rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/> <p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
<code> fix_modify AtC rates delete stress </code> <br/> <code> fix_modify AtC rates delete stress </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/> <p>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> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No rates are calculated by default </p> <p>No rates are calculated by default </p>
</div> </div>
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<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_initial">fix_modify AtC initial </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p> <p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li> <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li> <li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li> <li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p> <p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets the initial values for the specified field at the specified nodes. </p> <p>Sets the initial values for the specified field at the specified nodes. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p> <p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p> <p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p> <p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>on for coupling methods, off for post-processors off </p> <p>on for coupling methods, off for post-processors off </p>
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<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p> <p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
<ul> <ul>
<li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li> <li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p> <p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p> <p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p> <p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see atom_element_map_type and boundary </p> <p>see atom_element_map_type and boundary </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>off </p> <p>off </p>
</div> </div>
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<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p> <p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc internal_quadrature off </code> </p> <p><code> fix_modify atc internal_quadrature off </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p> <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"> <h4><a class="anchor" id="optional">
optional</a></h2> optional</a></h4>
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>on </p> <p>on </p>
</div> </div>
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<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p> <p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul> <ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/> <li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@ -28,21 +42,21 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/> quartic_sphere = radius (double) <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p> <p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/> <p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <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/> For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No default </p> <p>No default </p>
</div> </div>
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<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p> <p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc control localized_lambda on </code> <br/> <p><code> fix_modify atc control localized_lambda on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p> <p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Default is off. </p> <p>Default is off. </p>
</div> </div>
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<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p> <p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/> <p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to use or not use lumped matrix for lambda solve </p> <p>Command to use or not use lumped matrix for lambda solve </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p> <p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/> <p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to mask out certain dimensions from the atomic regulator </p> <p>Command to mask out certain dimensions from the atomic regulator </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p> <p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
<ul> <ul>
<li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li> <li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc mass_matrix fe </code> </p> <p><code> fix_modify atc mass_matrix fe </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p> <p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p> <p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Default is off </p> <p>Default is off </p>
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<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_material">fix_modify AtC material </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC material [elementset_name] [material_id] <br/> <p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC material gap_region 2</code> </p> <p><code> fix_modify AtC material gap_region 2</code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets the material model in elementset_name to be of type material_id. </p> <p>Sets the material model in elementset_name to be of type material_id. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p> <p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>All elements default to the first material in the material file. </p> <p>All elements default to the first material in the material file. </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p> <p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul> <ul>
<li>&lt;id&gt; = id of FE nodeset to be added to</li> <li>&lt;id&gt; = id of FE nodeset to be added to</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li> <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p> <p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to add nodes to an already existing FE nodeset. </p> <p>Command to add nodes to an already existing FE nodeset. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p> <p>Coordinates are assumed to be in lattice units. </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/> <p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
</p> </p>
<ul> <ul>
@ -20,21 +34,21 @@ syntax</a></h2>
<li>region-id = id of region that is to be meshed</li> <li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li> <li>f p p = periodicity flags for x, y, z </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/> <p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p> <p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Creates only uniform rectangular grids in a rectangular region </p> <p>Creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p> <p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p> <p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
</div> </div>
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<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p> <p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul> <ul>
<li>&lt;id&gt; = id to assign to the collection of FE element</li> <li>&lt;id&gt; = id to assign to the collection of FE element</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li> <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p> <p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p> <p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only viable for rectangular grids. </p> <p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p> <p>Coordinates are assumed to be in lattice units. </p>
</div> </div>
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<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p> <p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
<ul> <ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li> <li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@ -20,19 +34,19 @@ syntax</a></h2>
<li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li> <li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
<li>units = option to specify real as opposed to lattice units </li> <li>units = option to specify real as opposed to lattice units </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p> <p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to assign an id to a set of FE faces. </p> <p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only viable for rectangular grids. </p> <p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>The default options are units = lattice and the use of outer faces </p> <p>The default options are units = lattice and the use of outer faces </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p> <p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
<ul> <ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li> <li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@ -20,19 +34,19 @@ syntax</a></h2>
<li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li> <li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li> <li>units = option to specify real as opposed to lattice units </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p> <p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to assign an id to a set of FE faces. </p> <p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only viable for rectangular grids. </p> <p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>The default option is units = lattice. </p> <p>The default option is units = lattice. </p>
</div> </div>
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<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p> <p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul> <ul>
<li>&lt;id&gt; = id to assign to the collection of FE nodes</li> <li>&lt;id&gt; = id to assign to the collection of FE nodes</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li> <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p> <p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p> <p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p> <p>Coordinates are assumed to be in lattice units. </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p> <p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p>
<ul> <ul>
<li>&lt;element_set&gt; = name of an element set </li> <li>&lt;element_set&gt; = name of an element set </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC delete_elements gap </code> </p> <p><code> fix_modify AtC delete_elements gap </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Deletes a group of elements from the mesh. </p> <p>Deletes a group of elements from the mesh. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p> <p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p>
<ul> <ul>
<li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li> <li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li>
<li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li> <li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li>
<li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li> <li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p> <p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p> <p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>None. </p> <p>None. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Unless specified, the maximal element set is created </p> <p>Unless specified, the maximal element set is created </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh output &lt;file_prefix&gt; </p> <p>fix_modify AtC mesh output &lt;file_prefix&gt; </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh output meshData </code> <br/> <p><code> fix_modify AtC mesh output meshData </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>none </p> <p>none </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh quadrature &lt;quad&gt;</p> <p>fix_modify AtC mesh quadrature &lt;quad&gt;</p>
<ul> <ul>
<li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li> <li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh quadrature face </code> </p> <p><code> fix_modify AtC mesh quadrature face </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>(Re-)assigns the quadrature style for the existing mesh. </p> <p>(Re-)assigns the quadrature style for the existing mesh. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p> <p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p> <p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul> <ul>
<li>filename = name of file containing mesh to be read</li> <li>filename = name of file containing mesh to be read</li>
<li>f p p = periodicity flags for x, y, z </li> <li>f p p = periodicity flags for x, y, z </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/> <p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p> <code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p> <p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>periodicity flags are false by default </p> <p>periodicity flags are false by default </p>
</div> </div>
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<h1><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC mesh write &lt;filename&gt;</p> <p>fix_modify AtC mesh write &lt;filename&gt;</p>
<ul> <ul>
<li>filename = name of file to write mesh </li> <li>filename = name of file to write mesh </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/> <p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Writes a mesh to a text file. </p> <p>Writes a mesh to a text file. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp; <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
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<h1><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/> <p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p> </p>
<ul> <ul>
@ -21,24 +35,24 @@ syntax</a></h2>
</ul> </ul>
<p>various time integration methods for the finite elements<br/> <p>various time integration methods for the finite elements<br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/> <p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/> fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/> gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc time_integration verlet </code> <br/> <p><code> fix_modify atc time_integration verlet </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/> <code> fix_modify atc time_integration fractional_step </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_output">fix_modify AtC output </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p> <p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
<ul> <ul>
<li>filename_prefix (string) = prefix for data files</li> <li>filename_prefix (string) = prefix for data files</li>
@ -25,23 +39,23 @@ syntax</a></h2>
tensor_components = outputs tensor as scalar components (use this for Paraview)<br/> tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC output heatFE 100 </code> <br/> <p><code> fix_modify AtC output heatFE 100 </code> <br/>
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/> <code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/> <code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
<code> fix_modify AtC output index step </code> <br/> <code> fix_modify AtC output index step </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p> <p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>no default format output indexed by time </p> <p>no default format output indexed by time </p>
</div> </div>
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<h1><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p> <p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p>
<ul> <ul>
<li>set_name (string) = name of elementset to be integrated over</li> <li>set_name (string) = name of elementset to be integrated over</li>
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/> <li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC output eset1 mass_density </code> <br/> <p><code> fix_modify AtC output eset1 mass_density </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p> <p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp; <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

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USER-AtC Manual
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<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
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<h1><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p> <p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p>
<ul> <ul>
<li>nodeset_name (string) = name of nodeset to be operated on</li> <li>nodeset_name (string) = name of nodeset to be operated on</li>
@ -20,20 +34,20 @@ syntax</a></h2>
sum = creates nodal sum over nodes in specified nodeset <br/> sum = creates nodal sum over nodes in specified nodeset <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/> <p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p> <p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/> <p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/>
fix_modify AtC bond_interactions &lt;on|off&gt; <br/> fix_modify AtC bond_interactions &lt;on|off&gt; <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC bond_interactions on </code> <br/> <p><code> fix_modify AtC bond_interactions on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>include bonds and/or pairs in the stress and heat flux computations </p> <p>include bonds and/or pairs in the stress and heat flux computations </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>pair interactions: on, bond interactions: off </p> <p>pair interactions: on, bond interactions: off </p>
</div> </div>
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<hr>
<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p> <p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul> <ul>
<li>nx ny nz = number of elements in x, y, z</li> <li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li> <li>region-id = id of region that is to be meshed</li>
<li>f p p = perioidicity flags for x, y, z </li> <li>f p p = perioidicity flags for x, y, z </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p> <p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p> <p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>creates only uniform rectangular grids in a rectangular region </p> <p>creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC read_restart [file_name] <br/> <p>fix_modify AtC read_restart [file_name] <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC read_restart ATC_state </code> <br/> <p><code> fix_modify AtC read_restart ATC_state </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Reads the current state of the fields from a named text-based restart file. </p> <p>Reads the current state of the fields from a named text-based restart file. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p> <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"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p> <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"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/> <p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/>
</p> </p>
<ul> <ul>
<li>&lt;TAG&gt; = tag for tracking a molecule type <br/> <li>&lt;TAG&gt; = tag for tracking a molecule type <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC remove_molecule water </code> <br/> <p><code> fix_modify AtC remove_molecule water </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Removes tag designated for tracking a specified set of molecules. <br/> <p>Removes tag designated for tracking a specified set of molecules. <br/>
</p> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No defaults for this command. </p> <p>No defaults for this command. </p>
</div> </div>
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<!-- Generated by Doxygen 1.6.1 --> <!-- Generated by Doxygen 1.6.1 -->
<div class="contents"> <div class="contents">
<h1><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC remove_source &lt;field&gt; &lt;element_set&gt;</p> <p>fix_modify AtC remove_source &lt;field&gt; &lt;element_set&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics</li> <li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li> <li>&lt;element_set&gt; = name of set of elements </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc remove_source temperature groupNAME </code> </p> <p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Remove a domain source. </p> <p>Remove a domain source. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p> <p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p> <p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify_AtC delete_species &lt;TAG&gt; <br/> <p>fix_modify_AtC delete_species &lt;TAG&gt; <br/>
</p> </p>
<ul> <ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/> <li>&lt;TAG&gt; = tag for tracking a species <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC remove_species gold </code> <br/> <p><code> fix_modify AtC remove_species gold </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Removes tag designated for tracking a specified species. <br/> <p>Removes tag designated for tracking a specified species. <br/>
</p> </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>No defaults for this command. </p> <p>No defaults for this command. </p>
</div> </div>
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<h1><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC reset_atomic_reference_positions </p> <p>fix_modify AtC reset_atomic_reference_positions </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc reset_atomic_reference_positions </code></p> <p><code> fix_modify atc reset_atomic_reference_positions </code></p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p> <p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p><code> </code></p> <p><code> </code></p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><code> </code></p> <p><code> </code></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p><code> Default is off </code></p> <p><code> Default is off </code></p>
</div> </div>
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<h1><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC reset_time </p> <p>fix_modify AtC reset_time </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc reset_time 0.0 </code> <br/> <p><code> fix_modify atc reset_time 0.0 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Resets the simulation time counter. </p> <p>Resets the simulation time counter. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<h2><a class="anchor" id="syntax"> <h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC kernel_bandwidth </p> <p>fix_modify AtC kernel_bandwidth </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc reset_time 8 </code> <br/> <p><code> fix_modify atc reset_time 8 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p> <p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Only is used if kernel functions are being used. </p> <p>Only is used if kernel functions are being used. </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Number of sample locations. </p> <p>Number of sample locations. </p>
</div> </div>
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<h1><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC sample_frequency [freq]</p> <p>fix_modify AtC sample_frequency [freq]</p>
<ul> <ul>
<li>freq (int) : frequency to sample field in number of steps </li> <li>freq (int) : frequency to sample field in number of steps </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC sample_frequency 10 </code></p> <p><code> fix_modify AtC sample_frequency 10 </code></p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p> <p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p> <p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><code> </code></p> <p><code> </code></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p><code> none </code></p> <p><code> none </code></p>
</div> </div>
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<h1><a class="anchor" id="man_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_set">fix_modify AtC set </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p> <p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p>
<ul> <ul>
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/> <li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
</li> </li>
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li> <li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC set reference_potential_energy </code> <br/> <p><code> fix_modify AtC set reference_potential_energy </code> <br/>
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/> <code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/> <code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p> <p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p> <p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Defaults to lammps zero point i.e. isolated atoms </p> <p>Defaults to lammps zero point i.e. isolated atoms </p>
</div> </div>
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<h1><a class="anchor" id="man_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_source">fix_modify AtC source </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC source &lt;field&gt; &lt;element_set&gt; &lt;value | function&gt;</p> <p>fix_modify AtC source &lt;field&gt; &lt;element_set&gt; &lt;value | function&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics</li> <li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li> <li>&lt;element_set&gt; = name of set of elements </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p> <p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p> <p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p> <p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC source_integration &lt; fe | atom&gt; </p> <p>fix_modify AtC source_integration &lt; fe | atom&gt; </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc source_integration atom </code> </p> <p><code> fix_modify atc source_integration atom </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>Default is fe </p> <p>Default is fe </p>
</div> </div>
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<h1><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC temperature_definition &lt;kinetic|total&gt;</p> <p>fix_modify AtC temperature_definition &lt;kinetic|total&gt;</p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc temperature_definition kinetic </code> <br/> <p><code> fix_modify atc temperature_definition kinetic </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p> <p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p> <p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>kinetic </p> <p>kinetic </p>
</div> </div>
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<h1><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/> <p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p> </p>
<ul> <ul>
@ -21,23 +35,23 @@ syntax</a></h2>
</ul> </ul>
<p>various time integration methods for the finite elements<br/> <p>various time integration methods for the finite elements<br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/> <p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/> fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc time_integration gear </code> <br/> <p><code> fix_modify atc time_integration gear </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/> <code> fix_modify atc time_integration fractional_step </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p> <p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC filter &lt;on | off | equilibrate&gt; <br/> <p>fix_modify AtC filter &lt;on | off | equilibrate&gt; <br/>
</p> </p>
<ul> <ul>
@ -20,22 +34,22 @@ syntax</a></h2>
</li> </li>
<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li> <li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc transfer filter on </code> <br/> <p><code> fix_modify atc transfer filter on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p> <p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a> <br/> <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> <a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>off </p> <p>off </p>
</div> </div>
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<h1><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC track_displacement &lt;on/off&gt; <br/> <p>fix_modify AtC track_displacement &lt;on/off&gt; <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc track_displacement on </code> <br/> <p><code> fix_modify atc track_displacement on </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p> <p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>Some constitutive models require the displacement field </p> <p>Some constitutive models require the displacement field </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>on </p> <p>on </p>
</div> </div>
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<h1><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p> <p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li> <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li> <li>&lt;face_set&gt; = name of set of element faces </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/> <p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p> <p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p> <p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp; <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
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<h1><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC unfix &lt;field&gt; &lt;nodeset&gt;</p> <p>fix_modify AtC unfix &lt;field&gt; &lt;nodeset&gt;</p>
<ul> <ul>
<li>&lt;field&gt; = field name valid for type of physics</li> <li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes </li> <li>&lt;nodeset&gt; = name of set of nodes </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC unfix temperature groupNAME </code> </p> <p><code> fix_modify AtC unfix temperature groupNAME </code> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Removes constraint on field values for specified nodes. </p> <p>Removes constraint on field values for specified nodes. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p> <p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p> <p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
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<h1><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC write_atom_weights &lt;filename&gt; &lt;frequency&gt;</p> <p>fix_modify AtC write_atom_weights &lt;filename&gt; &lt;frequency&gt;</p>
<ul> <ul>
<li>&lt;filename&gt; = name of file that atomic weights are written to <br/> <li>&lt;filename&gt; = name of file that atomic weights are written to <br/>
@ -20,19 +34,19 @@ syntax</a></h2>
<li>&lt;frequency&gt; = how often writes will occur <br/> <li>&lt;frequency&gt; = how often writes will occur <br/>
</li> </li>
</ul> </ul>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/> <p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Command for writing the values of atomic weights to a specified file. </p> <p>Command for writing the values of atomic weights to a specified file. </p>
<h2><a class="anchor" id="restrictions"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<h2><a class="anchor" id="related"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<h2><a class="anchor" id="default"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
</div> </div>
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<h1><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h1><h2><a class="anchor" id="syntax"> <h3><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h2> syntax</a></h4>
<p>fix_modify AtC write_restart [file_name] <br/> <p>fix_modify AtC write_restart [file_name] <br/>
</p> </p>
<h2><a class="anchor" id="examples"> <h4><a class="anchor" id="examples">
examples</a></h2> examples</a></h4>
<p><code> fix_modify AtC write_restart restart.mydata </code> <br/> <p><code> fix_modify AtC write_restart restart.mydata </code> <br/>
</p> </p>
<h2><a class="anchor" id="description"> <h4><a class="anchor" id="description">
description</a></h2> description</a></h4>
<p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p> <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"> <h4><a class="anchor" id="restrictions">
restrictions</a></h2> restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p> <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"> <h4><a class="anchor" id="related">
related</a></h2> related</a></h4>
<p>see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a> </p> <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"> <h4><a class="anchor" id="default">
default</a></h2> default</a></h4>
<p>none </p> <p>none </p>
</div> </div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp; <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;